Starting phenix.real_space_refine on Sun Apr 27 15:54:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwy_43605/04_2025/8vwy_43605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwy_43605/04_2025/8vwy_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_43605/04_2025/8vwy_43605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwy_43605/04_2025/8vwy_43605.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwy_43605/04_2025/8vwy_43605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwy_43605/04_2025/8vwy_43605.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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: 4.74, per 1000 atoms: 0.75 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: 1.31 Conformation dependent library (CDL) restraints added in 921.8 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: 0.96 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: 1.63 Time building geometry restraints manager: 1.58 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 137 or re \ sid 201)) selection = (chain 'H' and (resid 6 through 68 or resid 70 through 137 or resid 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 137 or re \ sid 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.980 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.001 TRP B 31 HIS 0.003 0.001 HIS I 102 PHE 0.007 0.002 PHE I 55 TYR 0.019 0.002 TYR H 53 ARG 0.002 0.000 ARG E 17 Details of bonding type rmsd hydrogen bonds : bond 0.24366 ( 250) hydrogen bonds : angle 9.76773 ( 731) SS BOND : bond 0.00123 ( 15) SS BOND : angle 0.44138 ( 30) covalent geometry : bond 0.00640 ( 6438) covalent geometry : angle 0.58000 ( 8747) *********************** 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 : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7404 (m-30) cc_final: 0.6970 (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: 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: 0.7662 (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: 0.7047 time to fit residues: 133.6297 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 : 0.600 ------------------------------------------------------------------------------- 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 68 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4397 r_free = 0.4397 target = 0.198372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127076 restraints weight = 14159.283| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.31 r_work: 0.3456 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6453 Z= 0.149 Angle : 0.582 6.810 8777 Z= 0.308 Chirality : 0.043 0.150 964 Planarity : 0.003 0.044 1116 Dihedral : 7.023 56.498 905 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.07 % Allowed : 16.90 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.29), residues: 802 helix: 0.52 (0.54), residues: 93 sheet: -0.69 (0.28), residues: 334 loop : -1.22 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 31 HIS 0.004 0.001 HIS H 37 PHE 0.015 0.001 PHE C 101 TYR 0.016 0.001 TYR B 13 ARG 0.005 0.001 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 250) hydrogen bonds : angle 6.50861 ( 731) SS BOND : bond 0.00276 ( 15) SS BOND : angle 1.15523 ( 30) covalent geometry : bond 0.00326 ( 6438) covalent geometry : angle 0.57943 ( 8747) *********************** 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 178 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7190 (tppt) REVERT: A 96 GLN cc_start: 0.8262 (tt0) cc_final: 0.8008 (tm-30) REVERT: A 99 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7992 (tttp) REVERT: E 39 ASP cc_start: 0.7917 (t0) cc_final: 0.7473 (m-30) REVERT: E 41 THR cc_start: 0.6967 (p) cc_final: 0.6616 (m) REVERT: H 39 ASP cc_start: 0.7914 (t0) cc_final: 0.7482 (m-30) REVERT: H 41 THR cc_start: 0.7102 (p) cc_final: 0.6643 (m) REVERT: I 39 ASP cc_start: 0.7963 (t0) cc_final: 0.7509 (m-30) REVERT: I 41 THR cc_start: 0.7109 (p) cc_final: 0.6756 (m) REVERT: B 12 ILE cc_start: 0.7961 (mt) cc_final: 0.7710 (mp) REVERT: B 65 ASP cc_start: 0.7322 (m-30) cc_final: 0.6564 (t70) REVERT: B 97 TYR cc_start: 0.8467 (m-80) cc_final: 0.8190 (m-80) REVERT: B 138 SER cc_start: 0.4557 (p) cc_final: 0.4329 (t) REVERT: C 65 ASP cc_start: 0.7116 (m-30) cc_final: 0.6419 (t70) outliers start: 26 outliers final: 13 residues processed: 167 average time/residue: 0.7454 time to fit residues: 133.7164 Evaluate side-chains 155 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 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 77 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.197204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125218 restraints weight = 13597.089| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.31 r_work: 0.3447 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6453 Z= 0.165 Angle : 0.542 5.531 8777 Z= 0.289 Chirality : 0.043 0.172 964 Planarity : 0.003 0.032 1116 Dihedral : 6.295 57.430 893 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.91 % Allowed : 21.44 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.29), residues: 802 helix: 1.08 (0.54), residues: 90 sheet: -0.60 (0.27), residues: 331 loop : -1.40 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 31 HIS 0.004 0.001 HIS I 119 PHE 0.012 0.001 PHE C 101 TYR 0.018 0.001 TYR C 13 ARG 0.003 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 250) hydrogen bonds : angle 6.03612 ( 731) SS BOND : bond 0.00244 ( 15) SS BOND : angle 0.80160 ( 30) covalent geometry : bond 0.00364 ( 6438) covalent geometry : angle 0.54140 ( 8747) *********************** 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 178 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 ASP cc_start: 0.7941 (t0) cc_final: 0.7575 (m-30) REVERT: E 41 THR cc_start: 0.6969 (p) cc_final: 0.6627 (m) REVERT: H 39 ASP cc_start: 0.7876 (t0) cc_final: 0.7463 (m-30) REVERT: H 41 THR cc_start: 0.7083 (p) cc_final: 0.6625 (m) REVERT: I 39 ASP cc_start: 0.7944 (t0) cc_final: 0.7519 (m-30) REVERT: I 41 THR cc_start: 0.7052 (p) cc_final: 0.6694 (m) REVERT: B 12 ILE cc_start: 0.7963 (mt) cc_final: 0.7705 (mp) REVERT: B 34 GLU cc_start: 0.7488 (tt0) cc_final: 0.7225 (tt0) REVERT: B 65 ASP cc_start: 0.7333 (m-30) cc_final: 0.6663 (t70) REVERT: B 97 TYR cc_start: 0.8468 (m-80) cc_final: 0.8238 (m-80) REVERT: B 99 LYS cc_start: 0.8299 (ttmt) cc_final: 0.8048 (ttmt) REVERT: B 138 SER cc_start: 0.4815 (p) cc_final: 0.4589 (t) REVERT: C 34 GLU cc_start: 0.7576 (tt0) cc_final: 0.7345 (tt0) REVERT: C 65 ASP cc_start: 0.7080 (m-30) cc_final: 0.6509 (t70) REVERT: C 138 SER cc_start: 0.5118 (p) cc_final: 0.4816 (t) outliers start: 25 outliers final: 12 residues processed: 164 average time/residue: 0.7618 time to fit residues: 135.1236 Evaluate side-chains 152 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL 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 165 ILE Chi-restraints excluded: chain C residue 136 SER 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 38 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.198935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126475 restraints weight = 14734.613| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.51 r_work: 0.3462 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 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 = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6453 Z= 0.132 Angle : 0.520 7.674 8777 Z= 0.274 Chirality : 0.042 0.173 964 Planarity : 0.003 0.026 1116 Dihedral : 5.715 58.141 890 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.85 % Allowed : 22.07 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.29), residues: 802 helix: 1.39 (0.53), residues: 90 sheet: -0.55 (0.28), residues: 331 loop : -1.32 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 31 HIS 0.004 0.001 HIS I 119 PHE 0.012 0.001 PHE C 101 TYR 0.020 0.001 TYR C 13 ARG 0.002 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.02699 ( 250) hydrogen bonds : angle 5.71799 ( 731) SS BOND : bond 0.00191 ( 15) SS BOND : angle 0.59974 ( 30) covalent geometry : bond 0.00293 ( 6438) covalent geometry : angle 0.51926 ( 8747) *********************** 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 181 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6817 (mmm) cc_final: 0.5950 (tpp) REVERT: E 39 ASP cc_start: 0.7959 (t0) cc_final: 0.7598 (m-30) REVERT: E 41 THR cc_start: 0.6971 (p) cc_final: 0.6662 (m) REVERT: H 39 ASP cc_start: 0.7893 (t0) cc_final: 0.7474 (m-30) REVERT: H 41 THR cc_start: 0.7011 (p) cc_final: 0.6572 (m) REVERT: H 86 GLN cc_start: 0.8545 (tt0) cc_final: 0.8296 (tt0) REVERT: H 128 THR cc_start: 0.7742 (p) cc_final: 0.7524 (p) REVERT: I 39 ASP cc_start: 0.7974 (t0) cc_final: 0.7546 (m-30) REVERT: I 41 THR cc_start: 0.7045 (p) cc_final: 0.6727 (m) REVERT: B 12 ILE cc_start: 0.7952 (mt) cc_final: 0.7677 (mp) REVERT: B 34 GLU cc_start: 0.7476 (tt0) cc_final: 0.7229 (tt0) REVERT: B 65 ASP cc_start: 0.7336 (m-30) cc_final: 0.6631 (t70) REVERT: B 97 TYR cc_start: 0.8455 (m-80) cc_final: 0.8191 (m-80) REVERT: C 7 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6923 (tt) REVERT: C 65 ASP cc_start: 0.7160 (m-30) cc_final: 0.6512 (t70) REVERT: C 138 SER cc_start: 0.5017 (p) cc_final: 0.4752 (t) outliers start: 31 outliers final: 18 residues processed: 168 average time/residue: 0.6756 time to fit residues: 122.9033 Evaluate side-chains 157 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 98 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 68 SER 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 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 4 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 96 GLN A 100 ASN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN C 133 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.195677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123383 restraints weight = 13606.777| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.33 r_work: 0.3419 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 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 = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6453 Z= 0.211 Angle : 0.558 7.100 8777 Z= 0.295 Chirality : 0.043 0.166 964 Planarity : 0.003 0.024 1116 Dihedral : 5.988 57.837 889 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.63 % Allowed : 22.38 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 802 helix: 1.41 (0.54), residues: 93 sheet: -0.57 (0.28), residues: 331 loop : -1.33 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 31 HIS 0.005 0.001 HIS I 119 PHE 0.010 0.001 PHE C 140 TYR 0.023 0.002 TYR C 13 ARG 0.001 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.02806 ( 250) hydrogen bonds : angle 5.80530 ( 731) SS BOND : bond 0.00147 ( 15) SS BOND : angle 0.44125 ( 30) covalent geometry : bond 0.00471 ( 6438) covalent geometry : angle 0.55816 ( 8747) *********************** 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 162 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6777 (mmm) cc_final: 0.6056 (tpp) REVERT: E 39 ASP cc_start: 0.7968 (t0) cc_final: 0.7582 (m-30) REVERT: E 41 THR cc_start: 0.6980 (p) cc_final: 0.6662 (m) REVERT: H 39 ASP cc_start: 0.7880 (t0) cc_final: 0.7488 (m-30) REVERT: H 41 THR cc_start: 0.7061 (p) cc_final: 0.6624 (m) REVERT: H 96 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8406 (m) REVERT: I 20 GLU cc_start: 0.8334 (tt0) cc_final: 0.7654 (pm20) REVERT: I 39 ASP cc_start: 0.7926 (t0) cc_final: 0.7535 (m-30) REVERT: I 41 THR cc_start: 0.7038 (p) cc_final: 0.6695 (m) REVERT: B 12 ILE cc_start: 0.7984 (mt) cc_final: 0.7715 (mp) REVERT: B 65 ASP cc_start: 0.7298 (m-30) cc_final: 0.6681 (t70) REVERT: B 99 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8052 (tttp) REVERT: B 136 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8342 (p) REVERT: C 7 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6981 (tt) REVERT: C 65 ASP cc_start: 0.7164 (m-30) cc_final: 0.6533 (t70) outliers start: 36 outliers final: 20 residues processed: 149 average time/residue: 0.6876 time to fit residues: 110.8302 Evaluate side-chains 146 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 26 PHE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 SER 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 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 18 VAL 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 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 96 GLN A 100 ASN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 100 ASN C 63 GLN C 133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.199183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137963 restraints weight = 7852.184| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.88 r_work: 0.3530 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 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 = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6453 Z= 0.125 Angle : 0.517 7.608 8777 Z= 0.271 Chirality : 0.042 0.166 964 Planarity : 0.002 0.023 1116 Dihedral : 5.479 50.899 889 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.32 % Allowed : 23.32 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.29), residues: 802 helix: 1.87 (0.53), residues: 90 sheet: -0.55 (0.28), residues: 331 loop : -1.25 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 31 HIS 0.003 0.001 HIS I 119 PHE 0.011 0.001 PHE C 22 TYR 0.023 0.001 TYR C 13 ARG 0.001 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.02485 ( 250) hydrogen bonds : angle 5.52169 ( 731) SS BOND : bond 0.00148 ( 15) SS BOND : angle 0.38564 ( 30) covalent geometry : bond 0.00276 ( 6438) covalent geometry : angle 0.51698 ( 8747) *********************** 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 172 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6726 (mmm) cc_final: 0.6011 (tpp) REVERT: A 96 GLN cc_start: 0.8304 (tt0) cc_final: 0.7642 (tm-30) REVERT: A 99 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: E 39 ASP cc_start: 0.8042 (t0) cc_final: 0.7668 (m-30) REVERT: E 41 THR cc_start: 0.6988 (p) cc_final: 0.6701 (m) REVERT: H 39 ASP cc_start: 0.8002 (t0) cc_final: 0.7584 (m-30) REVERT: H 41 THR cc_start: 0.7067 (p) cc_final: 0.6653 (m) REVERT: I 39 ASP cc_start: 0.8071 (t0) cc_final: 0.7655 (m-30) REVERT: I 41 THR cc_start: 0.7012 (p) cc_final: 0.6724 (m) REVERT: B 12 ILE cc_start: 0.7950 (mt) cc_final: 0.7678 (mp) REVERT: B 65 ASP cc_start: 0.7325 (m-30) cc_final: 0.6697 (t70) REVERT: B 96 GLN cc_start: 0.8328 (tt0) cc_final: 0.8088 (tm-30) REVERT: B 99 LYS cc_start: 0.8266 (ttmt) cc_final: 0.8045 (tttp) REVERT: C 99 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7575 (tttp) outliers start: 34 outliers final: 16 residues processed: 163 average time/residue: 0.6592 time to fit residues: 116.3365 Evaluate side-chains 149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 165 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 124 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 96 GLN B 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.193072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127525 restraints weight = 9669.931| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.23 r_work: 0.3411 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 6453 Z= 0.340 Angle : 0.674 9.943 8777 Z= 0.352 Chirality : 0.046 0.158 964 Planarity : 0.004 0.049 1116 Dihedral : 6.205 59.189 889 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 5.32 % Allowed : 23.94 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.28), residues: 802 helix: 1.46 (0.55), residues: 93 sheet: -0.61 (0.28), residues: 331 loop : -1.54 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 31 HIS 0.007 0.002 HIS I 119 PHE 0.009 0.002 PHE I 55 TYR 0.027 0.002 TYR C 13 ARG 0.003 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 250) hydrogen bonds : angle 6.00072 ( 731) SS BOND : bond 0.00136 ( 15) SS BOND : angle 0.44320 ( 30) covalent geometry : bond 0.00763 ( 6438) covalent geometry : angle 0.67477 ( 8747) *********************** 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 160 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7505 (ttpt) cc_final: 0.6997 (tppt) REVERT: A 82 ILE cc_start: 0.5460 (OUTLIER) cc_final: 0.5125 (mp) REVERT: A 83 MET cc_start: 0.6774 (mmm) cc_final: 0.6188 (tpp) REVERT: A 99 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7828 (tttp) REVERT: E 39 ASP cc_start: 0.8115 (t0) cc_final: 0.7679 (m-30) REVERT: E 41 THR cc_start: 0.7036 (p) cc_final: 0.6732 (m) REVERT: E 80 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8207 (mmt90) REVERT: H 20 GLU cc_start: 0.8646 (tt0) cc_final: 0.7844 (pm20) REVERT: H 39 ASP cc_start: 0.8026 (t0) cc_final: 0.7581 (m-30) REVERT: H 41 THR cc_start: 0.7155 (p) cc_final: 0.6740 (m) REVERT: I 20 GLU cc_start: 0.8541 (tt0) cc_final: 0.7680 (pm20) REVERT: I 39 ASP cc_start: 0.8079 (t0) cc_final: 0.7640 (m-30) REVERT: I 41 THR cc_start: 0.7131 (p) cc_final: 0.6775 (m) REVERT: I 44 LYS cc_start: 0.8395 (mttt) cc_final: 0.8114 (mtmt) REVERT: B 12 ILE cc_start: 0.8033 (mt) cc_final: 0.7747 (mp) REVERT: B 65 ASP cc_start: 0.7361 (m-30) cc_final: 0.6653 (t70) REVERT: C 7 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7057 (tt) outliers start: 34 outliers final: 22 residues processed: 151 average time/residue: 0.7336 time to fit residues: 120.1426 Evaluate side-chains 142 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 99 LYS Chi-restraints excluded: chain A residue 165 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 96 GLN A 100 ASN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 63 GLN B 100 ASN C 63 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.199087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128192 restraints weight = 11726.394| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.06 r_work: 0.3492 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 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 = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6453 Z= 0.127 Angle : 0.542 6.838 8777 Z= 0.284 Chirality : 0.043 0.171 964 Planarity : 0.003 0.041 1116 Dihedral : 5.534 48.300 889 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.69 % Allowed : 24.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.28), residues: 802 helix: 1.97 (0.54), residues: 90 sheet: -0.55 (0.28), residues: 331 loop : -1.42 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 31 HIS 0.003 0.001 HIS I 37 PHE 0.012 0.001 PHE C 101 TYR 0.024 0.001 TYR B 13 ARG 0.001 0.000 ARG I 17 Details of bonding type rmsd hydrogen bonds : bond 0.02512 ( 250) hydrogen bonds : angle 5.58502 ( 731) SS BOND : bond 0.00151 ( 15) SS BOND : angle 0.40557 ( 30) covalent geometry : bond 0.00276 ( 6438) covalent geometry : angle 0.54227 ( 8747) *********************** 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 162 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7349 (ttpt) cc_final: 0.6412 (tptt) REVERT: A 83 MET cc_start: 0.6713 (mmm) cc_final: 0.5909 (tpp) REVERT: A 96 GLN cc_start: 0.8287 (tt0) cc_final: 0.7367 (tm-30) REVERT: A 99 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7561 (tttm) REVERT: E 39 ASP cc_start: 0.7939 (t0) cc_final: 0.7542 (m-30) REVERT: E 41 THR cc_start: 0.6966 (p) cc_final: 0.6685 (m) REVERT: H 39 ASP cc_start: 0.7903 (t0) cc_final: 0.7498 (m-30) REVERT: H 41 THR cc_start: 0.7055 (p) cc_final: 0.6644 (m) REVERT: I 39 ASP cc_start: 0.7984 (t0) cc_final: 0.7544 (m-30) REVERT: I 41 THR cc_start: 0.7019 (p) cc_final: 0.6702 (m) REVERT: B 12 ILE cc_start: 0.7954 (mt) cc_final: 0.7594 (mp) REVERT: C 99 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7143 (tttp) outliers start: 30 outliers final: 17 residues processed: 154 average time/residue: 0.6979 time to fit residues: 116.3300 Evaluate side-chains 145 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 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 9 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 18 optimal weight: 0.0570 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 100 ASN E 122 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 122 ASN I 124 ASN B 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.200345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129023 restraints weight = 11657.864| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.08 r_work: 0.3496 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 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 = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6453 Z= 0.122 Angle : 0.541 9.013 8777 Z= 0.280 Chirality : 0.043 0.169 964 Planarity : 0.003 0.038 1116 Dihedral : 5.353 42.728 887 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.44 % Allowed : 26.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.28), residues: 802 helix: 2.14 (0.53), residues: 90 sheet: -0.49 (0.27), residues: 331 loop : -1.34 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 31 HIS 0.003 0.001 HIS I 119 PHE 0.010 0.001 PHE B 140 TYR 0.024 0.001 TYR B 13 ARG 0.001 0.000 ARG I 62 Details of bonding type rmsd hydrogen bonds : bond 0.02450 ( 250) hydrogen bonds : angle 5.44757 ( 731) SS BOND : bond 0.00350 ( 15) SS BOND : angle 0.47844 ( 30) covalent geometry : bond 0.00272 ( 6438) covalent geometry : angle 0.54090 ( 8747) *********************** 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 150 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7293 (ttpt) cc_final: 0.6321 (tptt) REVERT: A 83 MET cc_start: 0.6738 (mmm) cc_final: 0.5941 (tpp) REVERT: A 96 GLN cc_start: 0.8124 (tt0) cc_final: 0.7573 (tm-30) REVERT: A 99 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7529 (tttm) REVERT: E 39 ASP cc_start: 0.7943 (t0) cc_final: 0.7585 (m-30) REVERT: E 41 THR cc_start: 0.6937 (p) cc_final: 0.6651 (m) REVERT: H 39 ASP cc_start: 0.7903 (t0) cc_final: 0.7475 (m-30) REVERT: H 41 THR cc_start: 0.6998 (p) cc_final: 0.6591 (m) REVERT: I 9 ILE cc_start: 0.8385 (mt) cc_final: 0.8135 (mt) REVERT: I 39 ASP cc_start: 0.7956 (t0) cc_final: 0.7519 (m-30) REVERT: I 41 THR cc_start: 0.6995 (p) cc_final: 0.6676 (m) REVERT: B 12 ILE cc_start: 0.7820 (mt) cc_final: 0.7488 (mp) outliers start: 22 outliers final: 14 residues processed: 145 average time/residue: 0.7062 time to fit residues: 110.5986 Evaluate side-chains 141 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 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 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 66 optimal weight: 0.0000 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 100 ASN E 122 ASN E 124 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN I 90 GLN I 122 ASN B 96 GLN B 100 ASN C 100 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.201418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129302 restraints weight = 13521.002| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.26 r_work: 0.3505 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6453 Z= 0.120 Angle : 0.540 9.260 8777 Z= 0.281 Chirality : 0.043 0.163 964 Planarity : 0.003 0.033 1116 Dihedral : 4.952 39.865 885 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.29 % Allowed : 26.76 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.28), residues: 802 helix: 2.23 (0.54), residues: 90 sheet: -0.50 (0.27), residues: 337 loop : -1.32 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 31 HIS 0.003 0.001 HIS I 119 PHE 0.011 0.001 PHE C 140 TYR 0.025 0.001 TYR B 13 ARG 0.002 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02441 ( 250) hydrogen bonds : angle 5.40104 ( 731) SS BOND : bond 0.00227 ( 15) SS BOND : angle 0.42171 ( 30) covalent geometry : bond 0.00270 ( 6438) covalent geometry : angle 0.53994 ( 8747) ********************** 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 148 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7278 (ttpt) cc_final: 0.6336 (tptt) REVERT: A 83 MET cc_start: 0.6725 (mmm) cc_final: 0.5853 (tpp) REVERT: A 96 GLN cc_start: 0.8113 (tt0) cc_final: 0.7619 (tm-30) REVERT: A 99 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7417 (tttm) REVERT: E 39 ASP cc_start: 0.7932 (t0) cc_final: 0.7613 (m-30) REVERT: E 41 THR cc_start: 0.6938 (p) cc_final: 0.6665 (m) REVERT: H 39 ASP cc_start: 0.7909 (t0) cc_final: 0.7487 (m-30) REVERT: H 41 THR cc_start: 0.6985 (p) cc_final: 0.6570 (m) REVERT: I 9 ILE cc_start: 0.8388 (mt) cc_final: 0.8152 (mt) REVERT: I 39 ASP cc_start: 0.7968 (t0) cc_final: 0.7589 (m-30) REVERT: I 41 THR cc_start: 0.6977 (p) cc_final: 0.6658 (m) REVERT: B 12 ILE cc_start: 0.7828 (mt) cc_final: 0.7573 (mp) REVERT: B 96 GLN cc_start: 0.8253 (tt0) cc_final: 0.7993 (tt0) outliers start: 21 outliers final: 13 residues processed: 144 average time/residue: 0.7357 time to fit residues: 114.1843 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 : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 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 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 78 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 76 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 0.0070 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 100 ASN C 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.201278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128884 restraints weight = 14433.693| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.36 r_work: 0.3488 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 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 = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6453 Z= 0.126 Angle : 0.546 6.865 8777 Z= 0.285 Chirality : 0.043 0.166 964 Planarity : 0.003 0.032 1116 Dihedral : 4.965 38.134 885 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.66 % Allowed : 27.54 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 802 helix: 2.29 (0.54), residues: 90 sheet: -0.42 (0.27), residues: 337 loop : -1.34 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 31 HIS 0.003 0.001 HIS I 119 PHE 0.016 0.001 PHE C 22 TYR 0.024 0.001 TYR B 13 ARG 0.004 0.000 ARG E 17 Details of bonding type rmsd hydrogen bonds : bond 0.02479 ( 250) hydrogen bonds : angle 5.39642 ( 731) SS BOND : bond 0.00187 ( 15) SS BOND : angle 0.39549 ( 30) covalent geometry : bond 0.00283 ( 6438) covalent geometry : angle 0.54665 ( 8747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6402.03 seconds wall clock time: 112 minutes 27.55 seconds (6747.55 seconds total)