Starting phenix.real_space_refine on Wed Sep 17 06:29:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwy_43605/09_2025/8vwy_43605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwy_43605/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vwy_43605/09_2025/8vwy_43605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwy_43605/09_2025/8vwy_43605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vwy_43605/09_2025/8vwy_43605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwy_43605/09_2025/8vwy_43605.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 7 9.91 5 S 52 5.16 5 C 4047 2.51 5 N 1016 2.21 5 O 1171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6293 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "H" Number of atoms: 1036 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1052 Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "B" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 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: 1.90, per 1000 atoms: 0.30 Number of scatterers: 6293 At special positions: 0 Unit cell: (99.256, 104.48, 78.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 7 19.99 S 52 16.00 O 1171 8.00 N 1016 7.00 C 4047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 29 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 29 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 29 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 152 " - pdb=" SG CYS C 163 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 391.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.25 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: 1.04 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1966 1.34 - 1.46: 1609 1.46 - 1.58: 2795 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 6438 Sorted by residual: bond pdb=" C PHE E 132 " pdb=" N ILE E 133 " ideal model delta sigma weight residual 1.329 1.304 0.025 1.46e-02 4.69e+03 2.83e+00 bond pdb=" CB VAL H 99 " pdb=" CG1 VAL H 99 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CB VAL E 99 " pdb=" CG1 VAL E 99 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CB VAL I 99 " pdb=" CG1 VAL I 99 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" C PHE I 132 " pdb=" N ILE I 133 " ideal model delta sigma weight residual 1.329 1.306 0.023 1.96e-02 2.60e+03 1.36e+00 ... (remaining 6433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 8262 1.14 - 2.27: 405 2.27 - 3.41: 58 3.41 - 4.55: 20 4.55 - 5.68: 2 Bond angle restraints: 8747 Sorted by residual: angle pdb=" C ASN E 76 " pdb=" CA ASN E 76 " pdb=" CB ASN E 76 " ideal model delta sigma weight residual 110.42 115.45 -5.03 1.99e+00 2.53e-01 6.39e+00 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 117.88 -3.98 1.80e+00 3.09e-01 4.89e+00 angle pdb=" CA TYR I 53 " pdb=" CB TYR I 53 " pdb=" CG TYR I 53 " ideal model delta sigma weight residual 113.90 117.70 -3.80 1.80e+00 3.09e-01 4.47e+00 angle pdb=" CA TYR H 53 " pdb=" CB TYR H 53 " pdb=" CG TYR H 53 " ideal model delta sigma weight residual 113.90 117.52 -3.62 1.80e+00 3.09e-01 4.04e+00 angle pdb=" N ASN E 76 " pdb=" CA ASN E 76 " pdb=" C ASN E 76 " ideal model delta sigma weight residual 110.80 106.58 4.22 2.13e+00 2.20e-01 3.92e+00 ... (remaining 8742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 3435 16.43 - 32.85: 245 32.85 - 49.27: 64 49.27 - 65.70: 8 65.70 - 82.12: 3 Dihedral angle restraints: 3755 sinusoidal: 1345 harmonic: 2410 Sorted by residual: dihedral pdb=" CA ASP H 29 " pdb=" C ASP H 29 " pdb=" N VAL H 30 " pdb=" CA VAL H 30 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LYS C 99 " pdb=" C LYS C 99 " pdb=" N ASN C 100 " pdb=" CA ASN C 100 " ideal model delta harmonic sigma weight residual -180.00 -164.42 -15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" CA ASP I 29 " pdb=" C ASP I 29 " pdb=" N VAL I 30 " pdb=" CA VAL I 30 " ideal model delta harmonic sigma weight residual -180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 3752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 516 0.027 - 0.053: 280 0.053 - 0.080: 95 0.080 - 0.106: 44 0.106 - 0.132: 29 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA ILE I 49 " pdb=" N ILE I 49 " pdb=" C ILE I 49 " pdb=" CB ILE I 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE H 49 " pdb=" N ILE H 49 " pdb=" C ILE H 49 " pdb=" CB ILE H 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA PRO H 40 " pdb=" N PRO H 40 " pdb=" C PRO H 40 " pdb=" CB PRO H 40 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 961 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 32 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C THR I 32 " -0.020 2.00e-02 2.50e+03 pdb=" O THR I 32 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN I 33 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 53 " -0.012 2.00e-02 2.50e+03 8.15e-03 1.33e+00 pdb=" CG TYR H 53 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 53 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 53 " 0.012 2.00e-02 2.50e+03 7.97e-03 1.27e+00 pdb=" CG TYR E 53 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 53 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 53 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 53 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 53 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 53 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 53 " 0.002 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 185 2.69 - 3.24: 5793 3.24 - 3.79: 10529 3.79 - 4.35: 14023 4.35 - 4.90: 23755 Nonbonded interactions: 54285 Sorted by model distance: nonbonded pdb=" OH TYR A 62 " pdb=" OE1 GLN A 103 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR C 62 " pdb=" OE1 GLN C 103 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR B 62 " pdb=" OE1 GLN B 103 " model vdw 2.136 3.040 nonbonded pdb=" OD1 ASP H 39 " pdb=" OG1 THR H 41 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP I 39 " pdb=" OG1 THR I 41 " model vdw 2.215 3.040 ... (remaining 54280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 4 through 173) selection = (chain 'C' and resid 4 through 173) } ncs_group { reference = (chain 'E' and (resid 6 through 68 or resid 70 through 122 or (resid 123 and (na \ me N or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'H' and (resid 6 through 68 or resid 70 through 201)) selection = (chain 'I' and (resid 6 through 68 or resid 70 through 122 or (resid 123 and (na \ me N or name CA or name C or name O or name CB )) or resid 124 through 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.930 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.28), residues: 802 helix: -0.16 (0.52), residues: 93 sheet: -0.60 (0.29), residues: 304 loop : -1.29 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 17 TYR 0.019 0.002 TYR H 53 PHE 0.007 0.002 PHE I 55 TRP 0.003 0.001 TRP B 31 HIS 0.003 0.001 HIS I 102 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 6438) covalent geometry : angle 0.58000 ( 8747) SS BOND : bond 0.00123 ( 15) SS BOND : angle 0.44138 ( 30) hydrogen bonds : bond 0.24366 ( 250) hydrogen bonds : angle 9.76773 ( 731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7404 (m-30) cc_final: 0.6958 (t70) REVERT: E 39 ASP cc_start: 0.8067 (t0) cc_final: 0.7698 (m-30) REVERT: E 41 THR cc_start: 0.7057 (p) cc_final: 0.6671 (m) REVERT: E 62 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7343 (mtp85) REVERT: H 20 GLU cc_start: 0.8512 (tt0) cc_final: 0.7712 (pm20) REVERT: H 39 ASP cc_start: 0.8037 (t0) cc_final: 0.7682 (m-30) REVERT: H 41 THR cc_start: 0.7094 (p) cc_final: 0.6715 (m) REVERT: I 20 GLU cc_start: 0.8458 (tt0) cc_final: 0.7661 (pm20) REVERT: I 39 ASP cc_start: 0.8012 (t0) cc_final: 0.7667 (m-30) REVERT: I 41 THR cc_start: 0.7280 (p) cc_final: 0.6867 (m) REVERT: B 12 ILE cc_start: 0.8023 (mt) cc_final: 0.7748 (mp) REVERT: B 65 ASP cc_start: 0.7189 (m-30) cc_final: 0.6840 (t70) REVERT: B 138 SER cc_start: 0.6019 (p) cc_final: 0.5658 (t) REVERT: C 65 ASP cc_start: 0.7272 (m-30) cc_final: 0.6952 (t70) outliers start: 39 outliers final: 18 residues processed: 176 average time/residue: 0.3416 time to fit residues: 64.6715 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 : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.198684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126776 restraints weight = 12630.215| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.23 r_work: 0.3464 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6453 Z= 0.147 Angle : 0.579 6.992 8777 Z= 0.307 Chirality : 0.043 0.149 964 Planarity : 0.003 0.042 1116 Dihedral : 7.016 56.363 905 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.23 % Allowed : 16.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.29), residues: 802 helix: 0.50 (0.54), residues: 93 sheet: -0.83 (0.27), residues: 343 loop : -1.11 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.016 0.001 TYR B 13 PHE 0.015 0.001 PHE C 101 TRP 0.010 0.001 TRP C 31 HIS 0.004 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6438) covalent geometry : angle 0.57689 ( 8747) SS BOND : bond 0.00256 ( 15) SS BOND : angle 1.05975 ( 30) hydrogen bonds : bond 0.03560 ( 250) hydrogen bonds : angle 6.48979 ( 731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7179 (tppt) REVERT: A 96 GLN cc_start: 0.8256 (tt0) cc_final: 0.8000 (tm-30) REVERT: A 99 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7790 (tttp) REVERT: E 39 ASP cc_start: 0.7914 (t0) cc_final: 0.7466 (m-30) REVERT: E 41 THR cc_start: 0.6965 (p) cc_final: 0.6609 (m) REVERT: H 39 ASP cc_start: 0.7905 (t0) cc_final: 0.7471 (m-30) REVERT: H 41 THR cc_start: 0.7101 (p) cc_final: 0.6637 (m) REVERT: H 86 GLN cc_start: 0.8532 (tt0) cc_final: 0.8233 (tt0) REVERT: I 39 ASP cc_start: 0.7945 (t0) cc_final: 0.7485 (m-30) REVERT: I 41 THR cc_start: 0.7109 (p) cc_final: 0.6752 (m) REVERT: B 12 ILE cc_start: 0.7963 (mt) cc_final: 0.7706 (mp) REVERT: B 65 ASP cc_start: 0.7319 (m-30) cc_final: 0.6558 (t70) REVERT: B 97 TYR cc_start: 0.8473 (m-80) cc_final: 0.8199 (m-80) REVERT: B 138 SER cc_start: 0.4548 (p) cc_final: 0.4321 (t) REVERT: C 65 ASP cc_start: 0.7108 (m-30) cc_final: 0.6412 (t70) outliers start: 27 outliers final: 13 residues processed: 169 average time/residue: 0.3365 time to fit residues: 61.1622 Evaluate side-chains 154 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 15 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN C 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.192788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127087 restraints weight = 18850.689| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 4.48 r_work: 0.3309 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 6453 Z= 0.292 Angle : 0.625 5.752 8777 Z= 0.334 Chirality : 0.045 0.160 964 Planarity : 0.003 0.029 1116 Dihedral : 6.947 58.082 893 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.54 % Allowed : 22.22 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.28), residues: 802 helix: 0.75 (0.53), residues: 93 sheet: -0.81 (0.27), residues: 352 loop : -1.49 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 80 TYR 0.020 0.002 TYR C 13 PHE 0.011 0.002 PHE C 101 TRP 0.016 0.002 TRP C 31 HIS 0.007 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 6438) covalent geometry : angle 0.62519 ( 8747) SS BOND : bond 0.00145 ( 15) SS BOND : angle 0.67912 ( 30) hydrogen bonds : bond 0.03524 ( 250) hydrogen bonds : angle 6.33422 ( 731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.5351 (OUTLIER) cc_final: 0.4994 (mp) REVERT: A 83 MET cc_start: 0.6834 (mmm) cc_final: 0.6027 (tpp) REVERT: A 99 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8064 (tttp) REVERT: E 39 ASP cc_start: 0.8032 (t0) cc_final: 0.7589 (m-30) REVERT: E 41 THR cc_start: 0.7058 (p) cc_final: 0.6699 (m) REVERT: H 39 ASP cc_start: 0.7978 (t0) cc_final: 0.7540 (m-30) REVERT: H 41 THR cc_start: 0.7155 (p) cc_final: 0.6692 (m) REVERT: I 20 GLU cc_start: 0.8524 (tt0) cc_final: 0.7715 (pm20) REVERT: I 39 ASP cc_start: 0.8050 (t0) cc_final: 0.7638 (m-30) REVERT: I 41 THR cc_start: 0.7153 (p) cc_final: 0.6760 (m) REVERT: B 12 ILE cc_start: 0.8066 (mt) cc_final: 0.7684 (mp) REVERT: B 65 ASP cc_start: 0.7422 (m-30) cc_final: 0.6766 (t70) REVERT: B 99 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8201 (ttmt) REVERT: C 65 ASP cc_start: 0.7237 (m-30) cc_final: 0.6547 (t70) REVERT: C 134 LYS cc_start: 0.7057 (mtmt) cc_final: 0.6832 (mtpt) outliers start: 29 outliers final: 17 residues processed: 148 average time/residue: 0.3223 time to fit residues: 51.5871 Evaluate side-chains 138 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 165 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 18 VAL 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 25 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 124 ASN I 33 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.198844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133654 restraints weight = 16956.113| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 4.41 r_work: 0.3441 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2355 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= 0.120 Angle : 0.521 8.374 8777 Z= 0.275 Chirality : 0.042 0.172 964 Planarity : 0.003 0.023 1116 Dihedral : 6.152 51.801 893 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.38 % Allowed : 22.85 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.28), residues: 802 helix: 1.20 (0.54), residues: 93 sheet: -0.61 (0.28), residues: 331 loop : -1.40 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 62 TYR 0.019 0.001 TYR C 13 PHE 0.013 0.001 PHE C 101 TRP 0.016 0.001 TRP C 31 HIS 0.004 0.001 HIS I 37 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6438) covalent geometry : angle 0.52145 ( 8747) SS BOND : bond 0.00174 ( 15) SS BOND : angle 0.48179 ( 30) hydrogen bonds : bond 0.02692 ( 250) hydrogen bonds : angle 5.70993 ( 731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6784 (mmm) cc_final: 0.5887 (tpp) REVERT: E 39 ASP cc_start: 0.7985 (t0) cc_final: 0.7566 (m-30) REVERT: E 41 THR cc_start: 0.6980 (p) cc_final: 0.6669 (m) REVERT: H 39 ASP cc_start: 0.7941 (t0) cc_final: 0.7524 (m-30) REVERT: H 41 THR cc_start: 0.7027 (p) cc_final: 0.6586 (m) REVERT: H 128 THR cc_start: 0.7690 (p) cc_final: 0.7428 (p) REVERT: I 39 ASP cc_start: 0.7978 (t0) cc_final: 0.7571 (m-30) REVERT: I 41 THR cc_start: 0.6997 (p) cc_final: 0.6682 (m) REVERT: B 12 ILE cc_start: 0.7958 (mt) cc_final: 0.7679 (mp) REVERT: B 34 GLU cc_start: 0.7485 (tt0) cc_final: 0.7206 (tt0) REVERT: B 65 ASP cc_start: 0.7260 (m-30) cc_final: 0.6632 (t70) REVERT: B 96 GLN cc_start: 0.8183 (tt0) cc_final: 0.7869 (tm-30) REVERT: B 99 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7948 (ttmt) REVERT: C 65 ASP cc_start: 0.7049 (m-30) cc_final: 0.6452 (t70) outliers start: 28 outliers final: 17 residues processed: 160 average time/residue: 0.3487 time to fit residues: 60.1654 Evaluate side-chains 147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 67 THR 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 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.195924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131188 restraints weight = 18803.420| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 4.37 r_work: 0.3346 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6453 Z= 0.207 Angle : 0.557 7.141 8777 Z= 0.294 Chirality : 0.043 0.162 964 Planarity : 0.003 0.022 1116 Dihedral : 6.153 55.266 892 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.54 % Allowed : 23.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.29), residues: 802 helix: 1.41 (0.55), residues: 93 sheet: -0.73 (0.27), residues: 340 loop : -1.37 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 62 TYR 0.022 0.002 TYR C 13 PHE 0.010 0.001 PHE C 140 TRP 0.016 0.002 TRP C 31 HIS 0.005 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6438) covalent geometry : angle 0.55759 ( 8747) SS BOND : bond 0.00144 ( 15) SS BOND : angle 0.43178 ( 30) hydrogen bonds : bond 0.02805 ( 250) hydrogen bonds : angle 5.73860 ( 731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6765 (mmm) cc_final: 0.6022 (tpp) REVERT: E 39 ASP cc_start: 0.8056 (t0) cc_final: 0.7633 (m-30) REVERT: E 41 THR cc_start: 0.7019 (p) cc_final: 0.6693 (m) REVERT: H 39 ASP cc_start: 0.7971 (t0) cc_final: 0.7549 (m-30) REVERT: H 41 THR cc_start: 0.7116 (p) cc_final: 0.6666 (m) REVERT: I 20 GLU cc_start: 0.8402 (tt0) cc_final: 0.7632 (pm20) REVERT: I 39 ASP cc_start: 0.8019 (t0) cc_final: 0.7580 (m-30) REVERT: I 41 THR cc_start: 0.7075 (p) cc_final: 0.6721 (m) REVERT: B 12 ILE cc_start: 0.8029 (mt) cc_final: 0.7752 (mp) REVERT: B 65 ASP cc_start: 0.7306 (m-30) cc_final: 0.6634 (t70) REVERT: B 136 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8421 (p) REVERT: C 7 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7012 (tt) REVERT: C 65 ASP cc_start: 0.7229 (m-30) cc_final: 0.6579 (t70) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.3471 time to fit residues: 54.5638 Evaluate side-chains 141 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 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 I residue 133 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 75 optimal weight: 0.0470 chunk 2 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 96 GLN B 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.199418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135555 restraints weight = 9669.267| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.06 r_work: 0.3506 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 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 = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2617 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= 0.114 Angle : 0.522 7.961 8777 Z= 0.272 Chirality : 0.042 0.166 964 Planarity : 0.003 0.037 1116 Dihedral : 5.754 48.845 891 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.60 % Allowed : 24.73 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.29), residues: 802 helix: 1.84 (0.53), residues: 90 sheet: -0.63 (0.27), residues: 340 loop : -1.25 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 62 TYR 0.023 0.001 TYR C 13 PHE 0.011 0.001 PHE C 101 TRP 0.015 0.001 TRP C 31 HIS 0.003 0.001 HIS I 37 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6438) covalent geometry : angle 0.52235 ( 8747) SS BOND : bond 0.00155 ( 15) SS BOND : angle 0.37685 ( 30) hydrogen bonds : bond 0.02485 ( 250) hydrogen bonds : angle 5.49355 ( 731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.246 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: 0.6813 (mmm) cc_final: 0.5951 (tpp) REVERT: A 96 GLN cc_start: 0.8286 (tt0) cc_final: 0.7641 (tm-30) REVERT: E 39 ASP cc_start: 0.7923 (t0) cc_final: 0.7568 (m-30) REVERT: E 41 THR cc_start: 0.6956 (p) cc_final: 0.6653 (m) REVERT: H 39 ASP cc_start: 0.7857 (t0) cc_final: 0.7426 (m-30) REVERT: H 41 THR cc_start: 0.7047 (p) cc_final: 0.6609 (m) REVERT: I 9 ILE cc_start: 0.8342 (mt) cc_final: 0.8078 (mt) REVERT: I 39 ASP cc_start: 0.7934 (t0) cc_final: 0.7486 (m-30) REVERT: I 41 THR cc_start: 0.7010 (p) cc_final: 0.6688 (m) REVERT: B 12 ILE cc_start: 0.7871 (mt) cc_final: 0.7601 (mp) REVERT: B 99 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7435 (tttp) REVERT: C 65 ASP cc_start: 0.7108 (m-30) cc_final: 0.6441 (t70) outliers start: 23 outliers final: 15 residues processed: 156 average time/residue: 0.3351 time to fit residues: 56.5694 Evaluate side-chains 144 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 E residue 130 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 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 96 GLN B 100 ASN C 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.195959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123916 restraints weight = 13589.113| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.22 r_work: 0.3427 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6453 Z= 0.211 Angle : 0.594 9.572 8777 Z= 0.310 Chirality : 0.044 0.183 964 Planarity : 0.003 0.073 1116 Dihedral : 5.701 53.220 888 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.16 % Allowed : 24.57 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.29), residues: 802 helix: 1.66 (0.54), residues: 90 sheet: -0.65 (0.27), residues: 340 loop : -1.36 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.025 0.002 TYR C 13 PHE 0.007 0.001 PHE E 129 TRP 0.022 0.002 TRP C 31 HIS 0.005 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 6438) covalent geometry : angle 0.58982 ( 8747) SS BOND : bond 0.00147 ( 15) SS BOND : angle 1.37853 ( 30) hydrogen bonds : bond 0.02725 ( 250) hydrogen bonds : angle 5.68471 ( 731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6783 (mmm) cc_final: 0.6099 (tpp) REVERT: E 39 ASP cc_start: 0.7957 (t0) cc_final: 0.7540 (m-30) REVERT: E 41 THR cc_start: 0.6973 (p) cc_final: 0.6660 (m) REVERT: H 39 ASP cc_start: 0.7925 (t0) cc_final: 0.7458 (m-30) REVERT: H 41 THR cc_start: 0.7091 (p) cc_final: 0.6645 (m) REVERT: I 20 GLU cc_start: 0.8249 (tt0) cc_final: 0.7585 (pm20) REVERT: I 39 ASP cc_start: 0.7951 (t0) cc_final: 0.7503 (m-30) REVERT: I 41 THR cc_start: 0.7047 (p) cc_final: 0.6681 (m) REVERT: I 44 LYS cc_start: 0.8307 (mttt) cc_final: 0.8034 (mtmt) REVERT: B 12 ILE cc_start: 0.7897 (mt) cc_final: 0.7547 (mp) REVERT: B 83 MET cc_start: 0.6894 (tpp) cc_final: 0.6609 (mmm) REVERT: C 7 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6989 (tt) REVERT: C 99 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7204 (tttp) outliers start: 33 outliers final: 25 residues processed: 151 average time/residue: 0.3119 time to fit residues: 51.1520 Evaluate side-chains 145 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 ASP 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 146 CYS 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 146 CYS Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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 ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4416 r_free = 0.4416 target = 0.199874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.128559 restraints weight = 13431.476| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.22 r_work: 0.3485 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6453 Z= 0.124 Angle : 0.538 8.013 8777 Z= 0.281 Chirality : 0.043 0.163 964 Planarity : 0.003 0.046 1116 Dihedral : 5.424 45.689 888 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.23 % Allowed : 25.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.29), residues: 802 helix: 1.83 (0.54), residues: 90 sheet: -0.56 (0.27), residues: 340 loop : -1.31 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 62 TYR 0.024 0.001 TYR C 13 PHE 0.009 0.001 PHE C 140 TRP 0.022 0.002 TRP C 31 HIS 0.003 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6438) covalent geometry : angle 0.53725 ( 8747) SS BOND : bond 0.00136 ( 15) SS BOND : angle 0.82146 ( 30) hydrogen bonds : bond 0.02488 ( 250) hydrogen bonds : angle 5.47139 ( 731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7282 (ttpt) cc_final: 0.6309 (tptt) REVERT: A 83 MET cc_start: 0.6734 (mmm) cc_final: 0.5923 (tpp) REVERT: A 96 GLN cc_start: 0.8355 (tt0) cc_final: 0.7894 (tt0) REVERT: A 99 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7568 (tttm) REVERT: E 39 ASP cc_start: 0.7955 (t0) cc_final: 0.7587 (m-30) REVERT: E 41 THR cc_start: 0.6966 (p) cc_final: 0.6678 (m) REVERT: H 39 ASP cc_start: 0.7908 (t0) cc_final: 0.7475 (m-30) REVERT: H 41 THR cc_start: 0.7020 (p) cc_final: 0.6594 (m) REVERT: I 9 ILE cc_start: 0.8420 (mt) cc_final: 0.8133 (mt) REVERT: I 39 ASP cc_start: 0.7951 (t0) cc_final: 0.7500 (m-30) REVERT: I 41 THR cc_start: 0.7008 (p) cc_final: 0.6700 (m) REVERT: B 12 ILE cc_start: 0.7832 (mt) cc_final: 0.7575 (mp) REVERT: B 34 GLU cc_start: 0.7454 (tt0) cc_final: 0.7193 (tt0) REVERT: C 99 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7475 (tttp) outliers start: 27 outliers final: 19 residues processed: 158 average time/residue: 0.3411 time to fit residues: 57.9895 Evaluate side-chains 151 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 67 THR 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 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 H residue 135 TYR Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 122 ASN B 96 GLN B 100 ASN C 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.197942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125147 restraints weight = 14496.652| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.33 r_work: 0.3452 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2797 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= 0.175 Angle : 0.578 9.183 8777 Z= 0.298 Chirality : 0.044 0.161 964 Planarity : 0.003 0.072 1116 Dihedral : 5.606 48.430 888 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.44 % Allowed : 26.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.29), residues: 802 helix: 1.94 (0.55), residues: 90 sheet: -0.62 (0.27), residues: 346 loop : -1.34 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.026 0.002 TYR I 94 PHE 0.012 0.001 PHE B 140 TRP 0.031 0.003 TRP A 31 HIS 0.005 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6438) covalent geometry : angle 0.57475 ( 8747) SS BOND : bond 0.00242 ( 15) SS BOND : angle 1.16250 ( 30) hydrogen bonds : bond 0.02590 ( 250) hydrogen bonds : angle 5.54923 ( 731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7317 (ttpt) cc_final: 0.6382 (tptt) REVERT: A 83 MET cc_start: 0.6753 (mmm) cc_final: 0.5952 (tpp) REVERT: A 96 GLN cc_start: 0.8267 (tt0) cc_final: 0.7497 (tm-30) REVERT: A 99 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7642 (tttm) REVERT: E 39 ASP cc_start: 0.7949 (t0) cc_final: 0.7569 (m-30) REVERT: E 41 THR cc_start: 0.6943 (p) cc_final: 0.6654 (m) REVERT: H 39 ASP cc_start: 0.7936 (t0) cc_final: 0.7488 (m-30) REVERT: H 41 THR cc_start: 0.7068 (p) cc_final: 0.6619 (m) REVERT: I 20 GLU cc_start: 0.8230 (tt0) cc_final: 0.7543 (pm20) REVERT: I 39 ASP cc_start: 0.7907 (t0) cc_final: 0.7530 (m-30) REVERT: I 41 THR cc_start: 0.7004 (p) cc_final: 0.6660 (m) REVERT: I 44 LYS cc_start: 0.8296 (mttt) cc_final: 0.8044 (mtmt) REVERT: B 12 ILE cc_start: 0.7901 (mt) cc_final: 0.7649 (mp) REVERT: C 7 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6918 (tt) REVERT: C 99 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7540 (tttp) REVERT: C 145 LEU cc_start: 0.7647 (mm) cc_final: 0.7445 (mm) outliers start: 22 outliers final: 20 residues processed: 143 average time/residue: 0.3063 time to fit residues: 47.5771 Evaluate side-chains 145 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 56 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 29 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 ASN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 122 ASN I 124 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 = 0.4421 r_free = 0.4421 target = 0.200717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128152 restraints weight = 15836.404| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.47 r_work: 0.3488 rms_B_bonded: 3.68 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 = 0.04 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 = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6453 Z= 0.120 Angle : 0.537 8.162 8777 Z= 0.279 Chirality : 0.043 0.162 964 Planarity : 0.003 0.054 1116 Dihedral : 5.368 42.513 888 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.60 % Allowed : 25.98 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.29), residues: 802 helix: 2.04 (0.55), residues: 90 sheet: -0.52 (0.27), residues: 337 loop : -1.33 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 62 TYR 0.025 0.001 TYR I 94 PHE 0.011 0.001 PHE C 140 TRP 0.032 0.003 TRP A 31 HIS 0.003 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6438) covalent geometry : angle 0.53449 ( 8747) SS BOND : bond 0.00173 ( 15) SS BOND : angle 1.04871 ( 30) hydrogen bonds : bond 0.02426 ( 250) hydrogen bonds : angle 5.39087 ( 731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7243 (ttpt) cc_final: 0.6280 (tptt) REVERT: A 83 MET cc_start: 0.6726 (mmm) cc_final: 0.5974 (tpp) REVERT: A 96 GLN cc_start: 0.8150 (tt0) cc_final: 0.7638 (tm-30) REVERT: A 99 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7573 (tttm) REVERT: E 39 ASP cc_start: 0.7955 (t0) cc_final: 0.7602 (m-30) REVERT: E 41 THR cc_start: 0.6976 (p) cc_final: 0.6702 (m) REVERT: H 39 ASP cc_start: 0.7919 (t0) cc_final: 0.7493 (m-30) REVERT: H 41 THR cc_start: 0.7063 (p) cc_final: 0.6634 (m) REVERT: I 9 ILE cc_start: 0.8408 (mt) cc_final: 0.8125 (mt) REVERT: I 39 ASP cc_start: 0.7972 (t0) cc_final: 0.7522 (m-30) REVERT: I 41 THR cc_start: 0.6995 (p) cc_final: 0.6686 (m) REVERT: B 12 ILE cc_start: 0.7849 (mt) cc_final: 0.7597 (mp) REVERT: C 99 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7526 (tttp) REVERT: C 145 LEU cc_start: 0.7649 (mm) cc_final: 0.7444 (mm) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.3598 time to fit residues: 56.3459 Evaluate side-chains 143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 114 ASP 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 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 77 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 122 ASN B 96 GLN B 100 ASN C 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.199152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133747 restraints weight = 16718.763| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 5.12 r_work: 0.3419 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6453 Z= 0.160 Angle : 0.566 7.771 8777 Z= 0.292 Chirality : 0.044 0.161 964 Planarity : 0.003 0.062 1116 Dihedral : 5.173 45.038 885 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.97 % Allowed : 26.92 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.29), residues: 802 helix: 2.08 (0.56), residues: 90 sheet: -0.53 (0.27), residues: 337 loop : -1.35 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 62 TYR 0.028 0.002 TYR I 94 PHE 0.012 0.001 PHE C 140 TRP 0.044 0.003 TRP C 31 HIS 0.004 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6438) covalent geometry : angle 0.56438 ( 8747) SS BOND : bond 0.00151 ( 15) SS BOND : angle 0.96530 ( 30) hydrogen bonds : bond 0.02521 ( 250) hydrogen bonds : angle 5.49725 ( 731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.89 seconds wall clock time: 47 minutes 15.26 seconds (2835.26 seconds total)