Starting phenix.real_space_refine on Thu Jun 4 01:54:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkp_74380/06_2026/9zkp_74380.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkp_74380/06_2026/9zkp_74380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zkp_74380/06_2026/9zkp_74380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkp_74380/06_2026/9zkp_74380.map" model { file = "/net/cci-nas-00/data/ceres_data/9zkp_74380/06_2026/9zkp_74380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkp_74380/06_2026/9zkp_74380.cif" } resolution = 2.87 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 65 5.16 5 C 6469 2.51 5 N 1385 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9502 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1032 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1049 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 984 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1361 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Chain: "H" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1361 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Chain: "A" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 197 Unusual residues: {'OLC': 3, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {'OLC': 1, 'PLM': 3, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 195 Unusual residues: {'OLC': 3, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'OLC': 1, 'PLM': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.22, per 1000 atoms: 0.23 Number of scatterers: 9502 At special positions: 0 Unit cell: (101.475, 100.65, 85.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 8 15.00 O 1575 8.00 N 1385 7.00 C 6469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " 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: 0.89 Conformation dependent library (CDL) restraints added in 364.8 milliseconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 2 sheets defined 79.0% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.748A pdb=" N LEU A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 626 removed outlier: 3.639A pdb=" N VAL A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.536A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.840A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.562A pdb=" N SER B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.573A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 625 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.548A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.845A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.514A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 removed outlier: 3.664A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 85 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 87 through 108 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 127 through 159 Processing helix chain 'F' and resid 3 through 37 removed outlier: 4.064A pdb=" N ALA F 7 " --> pdb=" O PHE F 3 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 85 Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 87 through 108 Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 127 through 159 Processing helix chain 'G' and resid 16 through 41 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 128 through 151 removed outlier: 3.900A pdb=" N ARG G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 183 removed outlier: 4.059A pdb=" N LEU G 159 " --> pdb=" O ARG G 155 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN G 183 " --> pdb=" O TYR G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 235 removed outlier: 3.758A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 41 Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 128 through 151 removed outlier: 3.868A pdb=" N ARG H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 182 removed outlier: 4.090A pdb=" N LEU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA H 168 " --> pdb=" O LEU H 164 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE H 174 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA H 182 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 235 removed outlier: 3.768A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'H' and resid 100 through 102 738 hydrogen bonds defined for protein. 2193 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: 1.46 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1671 1.33 - 1.46: 3082 1.46 - 1.59: 4839 1.59 - 1.72: 16 1.72 - 1.84: 88 Bond restraints: 9696 Sorted by residual: bond pdb=" O12 POV E 201 " pdb=" P POV E 201 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" O12 POV A1004 " pdb=" P POV A1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" O12 POV C 905 " pdb=" P POV C 905 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" O12 POV B1002 " pdb=" P POV B1002 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" O12 POV F 201 " pdb=" P POV F 201 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.45e+00 ... (remaining 9691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 12643 2.03 - 4.06: 272 4.06 - 6.09: 49 6.09 - 8.12: 18 8.12 - 10.15: 1 Bond angle restraints: 12983 Sorted by residual: angle pdb=" CA GLU F 134 " pdb=" CB GLU F 134 " pdb=" CG GLU F 134 " ideal model delta sigma weight residual 114.10 124.25 -10.15 2.00e+00 2.50e-01 2.58e+01 angle pdb=" N GLU E 134 " pdb=" CA GLU E 134 " pdb=" CB GLU E 134 " ideal model delta sigma weight residual 110.40 118.51 -8.11 1.63e+00 3.76e-01 2.48e+01 angle pdb=" N GLN F 132 " pdb=" CA GLN F 132 " pdb=" CB GLN F 132 " ideal model delta sigma weight residual 110.39 118.31 -7.92 1.66e+00 3.63e-01 2.28e+01 angle pdb=" CB GLU F 134 " pdb=" CG GLU F 134 " pdb=" CD GLU F 134 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.70e+00 3.46e-01 1.45e+01 angle pdb=" N GLU F 134 " pdb=" CA GLU F 134 " pdb=" CB GLU F 134 " ideal model delta sigma weight residual 110.40 116.45 -6.05 1.63e+00 3.76e-01 1.38e+01 ... (remaining 12978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 5470 34.78 - 69.57: 112 69.57 - 104.35: 19 104.35 - 139.13: 17 139.13 - 173.92: 4 Dihedral angle restraints: 5622 sinusoidal: 2353 harmonic: 3269 Sorted by residual: dihedral pdb=" C3 POV H 501 " pdb=" C31 POV H 501 " pdb=" O31 POV H 501 " pdb=" C32 POV H 501 " ideal model delta sinusoidal sigma weight residual 172.61 -1.31 173.92 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 POV C 904 " pdb=" C31 POV C 904 " pdb=" O31 POV C 904 " pdb=" C32 POV C 904 " ideal model delta sinusoidal sigma weight residual 172.61 -0.58 173.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 POV A1003 " pdb=" C31 POV A1003 " pdb=" O31 POV A1003 " pdb=" C32 POV A1003 " ideal model delta sinusoidal sigma weight residual 172.61 0.52 172.09 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1062 0.043 - 0.085: 312 0.085 - 0.127: 63 0.127 - 0.170: 6 0.170 - 0.212: 4 Chirality restraints: 1447 Sorted by residual: chirality pdb=" C2 POV E 201 " pdb=" C1 POV E 201 " pdb=" C3 POV E 201 " pdb=" O21 POV E 201 " both_signs ideal model delta sigma weight residual False 2.43 2.22 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU E 144 " pdb=" CB LEU E 144 " pdb=" CD1 LEU E 144 " pdb=" CD2 LEU E 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CA GLU E 134 " pdb=" N GLU E 134 " pdb=" C GLU E 134 " pdb=" CB GLU E 134 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 1444 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 626 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C VAL D 626 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL D 626 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU D 627 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 626 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C VAL B 626 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL B 626 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 627 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO D 520 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " 0.030 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 381 2.73 - 3.27: 9435 3.27 - 3.81: 15976 3.81 - 4.36: 18329 4.36 - 4.90: 32554 Nonbonded interactions: 76675 Sorted by model distance: nonbonded pdb=" O GLN H 20 " pdb=" OG1 THR H 24 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR G 82 " pdb=" O CYS G 90 " model vdw 2.279 3.040 nonbonded pdb=" O LEU E 16 " pdb=" OG SER E 19 " model vdw 2.281 3.040 nonbonded pdb=" O GLY B 572 " pdb=" OG SER B 576 " model vdw 2.374 3.040 nonbonded pdb=" O ILE G 37 " pdb=" OG1 THR G 41 " model vdw 2.380 3.040 ... (remaining 76670 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' and (resid 507 through 543 or (resid 565 and (name N or name CA or na \ me C or name O or name CB )) or resid 566 through 581 or resid 583 through 624 o \ r resid 780 through 795 or resid 797 through 811 or (resid 812 through 813 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 585 or resid 587 through 628 or (resid 784 and (name N \ or name CA or name C or name O or name CB )) or resid 785 through 799 or resid 8 \ 01 through 817)) selection = (chain 'C' and (resid 507 through 543 or (resid 565 and (name N or name CA or na \ me C or name O or name CB )) or resid 566 through 581 or resid 583 through 624 o \ r resid 780 through 795 or resid 797 through 811 or (resid 812 through 813 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 585 or resid 587 through 628 or (resid 784 and (name N \ or name CA or name C or name O or name CB )) or resid 785 through 799 or resid 8 \ 01 through 817)) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 201 and (name C1 or name C2 or nam \ e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P or name C310 or name C311)))) selection = (chain 'F' and (resid 2 through 106 or (resid 107 through 108 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 201)) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 15 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.870 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 0.055 9700 Z= 0.285 Angle : 0.750 10.149 12991 Z= 0.376 Chirality : 0.042 0.212 1447 Planarity : 0.005 0.052 1508 Dihedral : 17.750 173.917 3508 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.11 % Allowed : 0.00 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.24), residues: 1087 helix: 1.92 (0.16), residues: 881 sheet: -4.01 (1.04), residues: 10 loop : -1.26 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 590 TYR 0.028 0.002 TYR G 226 PHE 0.025 0.002 PHE B 574 TRP 0.011 0.001 TRP A 601 HIS 0.013 0.003 HIS F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.28 ( 9696) covalent geometry : angle 0.74877 / 0.38 (12983) SS BOND : bond 0.00337 / 0.17 ( 4) SS BOND : angle 2.14170 / 1.83 ( 8) hydrogen bonds : bond 0.09674 / 6.52 ( 738) hydrogen bonds : angle 4.41854 / 3.19 ( 2193) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 541 ARG cc_start: 0.6278 (mmt-90) cc_final: 0.5590 (mtp180) REVERT: A 566 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5507 (pm20) REVERT: A 590 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.6358 (mtm110) REVERT: B 516 SER cc_start: 0.7496 (m) cc_final: 0.7168 (p) REVERT: B 527 MET cc_start: 0.6758 (mmm) cc_final: 0.6346 (mmp) REVERT: B 585 MET cc_start: 0.6710 (mmt) cc_final: 0.6061 (mmt) REVERT: B 788 SER cc_start: 0.7711 (t) cc_final: 0.7240 (p) REVERT: C 541 ARG cc_start: 0.5857 (mmp-170) cc_final: 0.5501 (mtp180) REVERT: C 590 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.6723 (mtm110) REVERT: D 585 MET cc_start: 0.6622 (mmt) cc_final: 0.6045 (mmt) REVERT: E 88 TRP cc_start: 0.4663 (m-10) cc_final: 0.4049 (m100) REVERT: F 67 LEU cc_start: 0.7224 (mm) cc_final: 0.6994 (tp) REVERT: F 88 TRP cc_start: 0.4613 (m-10) cc_final: 0.3986 (m100) REVERT: G 88 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6360 (mtm-85) REVERT: G 122 ARG cc_start: 0.5549 (mmt90) cc_final: 0.5196 (mmt-90) REVERT: H 43 TYR cc_start: 0.7636 (m-80) cc_final: 0.7044 (m-80) REVERT: H 88 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6337 (mtm-85) REVERT: H 96 LYS cc_start: 0.3798 (mppt) cc_final: 0.3549 (mtmt) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.4662 time to fit residues: 63.9018 Evaluate side-chains 96 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 791 ASN E 75 HIS E 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN H 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.193633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143751 restraints weight = 9602.458| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.60 r_work: 0.3438 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9700 Z= 0.121 Angle : 0.460 5.069 12991 Z= 0.249 Chirality : 0.035 0.129 1447 Planarity : 0.003 0.038 1508 Dihedral : 16.134 173.322 1740 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.97 % Allowed : 4.91 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.25), residues: 1087 helix: 2.71 (0.17), residues: 883 sheet: -4.11 (0.94), residues: 10 loop : -1.10 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 590 TYR 0.020 0.001 TYR G 226 PHE 0.019 0.001 PHE B 574 TRP 0.008 0.001 TRP C 574 HIS 0.011 0.002 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9696) covalent geometry : angle 0.46022 / 0.25 (12983) SS BOND : bond 0.00370 / 0.19 ( 4) SS BOND : angle 0.71920 / 0.58 ( 8) hydrogen bonds : bond 0.04251 / 2.78 ( 738) hydrogen bonds : angle 3.43213 / 2.46 ( 2193) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6344 (pm20) REVERT: A 590 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.7850 (mtm110) REVERT: B 585 MET cc_start: 0.8559 (mmt) cc_final: 0.7838 (mmt) REVERT: C 566 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6418 (pm20) REVERT: C 590 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.7977 (mtm110) REVERT: D 585 MET cc_start: 0.8633 (mmt) cc_final: 0.7794 (mmt) REVERT: D 586 ARG cc_start: 0.8185 (mmt90) cc_final: 0.7980 (mmp-170) REVERT: E 88 TRP cc_start: 0.5714 (m-10) cc_final: 0.5159 (m100) REVERT: E 149 TYR cc_start: 0.7027 (m-10) cc_final: 0.6759 (m-10) REVERT: F 88 TRP cc_start: 0.5763 (m-10) cc_final: 0.5232 (m100) REVERT: G 88 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7383 (mtm-85) REVERT: G 122 ARG cc_start: 0.7171 (mmt90) cc_final: 0.6776 (mmt-90) REVERT: H 23 LEU cc_start: 0.6169 (tp) cc_final: 0.5866 (mt) REVERT: H 88 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7339 (mtm-85) outliers start: 18 outliers final: 8 residues processed: 110 average time/residue: 0.5176 time to fit residues: 61.4490 Evaluate side-chains 104 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 ASN F 75 HIS F 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.195428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151366 restraints weight = 9592.891| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.87 r_work: 0.3496 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9700 Z= 0.145 Angle : 0.469 5.079 12991 Z= 0.251 Chirality : 0.036 0.127 1447 Planarity : 0.003 0.034 1508 Dihedral : 14.908 178.148 1740 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.29 % Allowed : 6.88 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.25), residues: 1087 helix: 2.79 (0.17), residues: 884 sheet: -3.45 (0.72), residues: 20 loop : -1.14 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.022 0.001 TYR G 226 PHE 0.014 0.001 PHE C 542 TRP 0.007 0.001 TRP C 574 HIS 0.007 0.002 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9696) covalent geometry : angle 0.46897 / 0.25 (12983) SS BOND : bond 0.00238 / 0.12 ( 4) SS BOND : angle 0.76488 / 0.44 ( 8) hydrogen bonds : bond 0.04324 / 2.82 ( 738) hydrogen bonds : angle 3.37751 / 2.41 ( 2193) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7812 (mtm110) REVERT: B 585 MET cc_start: 0.8524 (mmt) cc_final: 0.7662 (mmt) REVERT: C 566 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6658 (pm20) REVERT: C 590 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.7951 (mtm110) REVERT: D 585 MET cc_start: 0.8638 (mmt) cc_final: 0.8318 (mmt) REVERT: D 586 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7987 (mmp-170) REVERT: E 88 TRP cc_start: 0.5701 (m-10) cc_final: 0.5277 (m100) REVERT: E 144 LEU cc_start: 0.7019 (mp) cc_final: 0.6809 (mm) REVERT: F 88 TRP cc_start: 0.5711 (m-10) cc_final: 0.5303 (m100) REVERT: F 94 ASN cc_start: 0.7679 (m-40) cc_final: 0.7447 (m-40) REVERT: G 88 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7248 (mtm-85) REVERT: G 122 ARG cc_start: 0.7178 (mmt90) cc_final: 0.6824 (mmt-90) REVERT: H 88 ARG cc_start: 0.7498 (mtm-85) cc_final: 0.7258 (mtm-85) REVERT: H 200 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7820 (p) outliers start: 21 outliers final: 9 residues processed: 110 average time/residue: 0.5532 time to fit residues: 65.4273 Evaluate side-chains 106 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 200 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.0060 chunk 9 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 ASN F 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.196409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152919 restraints weight = 9706.310| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.87 r_work: 0.3498 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9700 Z= 0.114 Angle : 0.425 5.612 12991 Z= 0.227 Chirality : 0.035 0.121 1447 Planarity : 0.003 0.032 1508 Dihedral : 14.355 175.168 1740 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.18 % Allowed : 8.41 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.25), residues: 1087 helix: 3.03 (0.17), residues: 887 sheet: -5.17 (0.57), residues: 10 loop : -1.04 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 628 TYR 0.024 0.001 TYR F 149 PHE 0.020 0.001 PHE E 106 TRP 0.008 0.001 TRP G 203 HIS 0.007 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9696) covalent geometry : angle 0.42471 / 0.23 (12983) SS BOND : bond 0.00192 / 0.10 ( 4) SS BOND : angle 0.77248 / 0.52 ( 8) hydrogen bonds : bond 0.03989 / 2.61 ( 738) hydrogen bonds : angle 3.20993 / 2.30 ( 2193) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.7946 (mtm110) REVERT: B 585 MET cc_start: 0.8568 (mmt) cc_final: 0.7760 (mmt) REVERT: C 566 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6655 (pm20) REVERT: C 590 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8104 (mtm110) REVERT: D 586 ARG cc_start: 0.8288 (mmt90) cc_final: 0.8056 (mmp-170) REVERT: E 88 TRP cc_start: 0.5772 (m-10) cc_final: 0.5191 (m100) REVERT: E 144 LEU cc_start: 0.7199 (mp) cc_final: 0.6991 (mm) REVERT: E 149 TYR cc_start: 0.7277 (m-10) cc_final: 0.7026 (m-10) REVERT: F 88 TRP cc_start: 0.5842 (m-10) cc_final: 0.5289 (m100) REVERT: F 94 ASN cc_start: 0.7786 (m-40) cc_final: 0.7551 (m-40) REVERT: G 88 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: H 23 LEU cc_start: 0.6201 (tp) cc_final: 0.5917 (mt) REVERT: H 88 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7422 (mtm-85) REVERT: H 155 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6263 (ttm170) REVERT: H 200 SER cc_start: 0.8239 (t) cc_final: 0.7997 (p) outliers start: 20 outliers final: 11 residues processed: 112 average time/residue: 0.5133 time to fit residues: 61.8283 Evaluate side-chains 114 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 155 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 98 optimal weight: 0.0020 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.195561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151239 restraints weight = 9735.816| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.82 r_work: 0.3503 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9700 Z= 0.119 Angle : 0.432 6.459 12991 Z= 0.229 Chirality : 0.035 0.122 1447 Planarity : 0.003 0.032 1508 Dihedral : 14.093 160.124 1740 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.18 % Allowed : 9.28 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.25), residues: 1087 helix: 3.14 (0.16), residues: 886 sheet: -5.52 (0.50), residues: 10 loop : -1.03 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 155 TYR 0.026 0.001 TYR F 149 PHE 0.012 0.001 PHE E 31 TRP 0.007 0.001 TRP G 203 HIS 0.006 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9696) covalent geometry : angle 0.43149 / 0.23 (12983) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 0.77810 / 0.54 ( 8) hydrogen bonds : bond 0.03979 / 2.60 ( 738) hydrogen bonds : angle 3.18847 / 2.28 ( 2193) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.7831 (mtm110) REVERT: B 585 MET cc_start: 0.8481 (mmt) cc_final: 0.7702 (mmt) REVERT: C 566 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6657 (pm20) REVERT: C 590 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.7952 (mtm110) REVERT: F 88 TRP cc_start: 0.5707 (m-10) cc_final: 0.5292 (m100) REVERT: F 94 ASN cc_start: 0.7803 (m-40) cc_final: 0.7529 (m-40) REVERT: H 23 LEU cc_start: 0.6189 (tp) cc_final: 0.5906 (mt) REVERT: H 88 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7296 (mtm-85) REVERT: H 155 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.6240 (ttm170) REVERT: H 200 SER cc_start: 0.8085 (t) cc_final: 0.7831 (p) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 0.4998 time to fit residues: 58.8910 Evaluate side-chains 111 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 155 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149744 restraints weight = 9654.529| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.87 r_work: 0.3457 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9700 Z= 0.146 Angle : 0.467 6.897 12991 Z= 0.245 Chirality : 0.036 0.128 1447 Planarity : 0.003 0.034 1508 Dihedral : 14.304 153.579 1740 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.75 % Allowed : 10.15 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.25), residues: 1087 helix: 3.05 (0.16), residues: 885 sheet: -5.60 (0.52), residues: 10 loop : -1.09 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.024 0.001 TYR F 149 PHE 0.011 0.001 PHE F 8 TRP 0.007 0.001 TRP E 103 HIS 0.006 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 9696) covalent geometry : angle 0.46677 / 0.24 (12983) SS BOND : bond 0.00224 / 0.11 ( 4) SS BOND : angle 0.78120 / 0.51 ( 8) hydrogen bonds : bond 0.04171 / 2.73 ( 738) hydrogen bonds : angle 3.31015 / 2.35 ( 2193) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8547 (mtm-85) cc_final: 0.7958 (mtm110) REVERT: B 585 MET cc_start: 0.8614 (mmt) cc_final: 0.7792 (mmt) REVERT: C 566 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6674 (pm20) REVERT: C 590 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8071 (mtm110) REVERT: D 585 MET cc_start: 0.8832 (mmt) cc_final: 0.7787 (mmt) REVERT: E 94 ASN cc_start: 0.7821 (m-40) cc_final: 0.7561 (m-40) REVERT: F 88 TRP cc_start: 0.5800 (m-10) cc_final: 0.5260 (m100) REVERT: F 94 ASN cc_start: 0.7811 (m-40) cc_final: 0.7542 (m-40) REVERT: G 88 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7507 (mtm-85) REVERT: H 23 LEU cc_start: 0.6294 (tp) cc_final: 0.6000 (mt) REVERT: H 88 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: H 155 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6279 (ttm170) REVERT: H 200 SER cc_start: 0.8235 (t) cc_final: 0.7979 (p) outliers start: 16 outliers final: 12 residues processed: 105 average time/residue: 0.5849 time to fit residues: 65.9143 Evaluate side-chains 109 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 155 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.191917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147924 restraints weight = 9710.900| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.76 r_work: 0.3452 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9700 Z= 0.176 Angle : 0.515 9.238 12991 Z= 0.266 Chirality : 0.038 0.134 1447 Planarity : 0.003 0.036 1508 Dihedral : 14.737 147.463 1740 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.62 % Allowed : 10.04 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.25), residues: 1087 helix: 2.89 (0.16), residues: 880 sheet: -5.57 (0.57), residues: 10 loop : -1.12 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 628 TYR 0.027 0.002 TYR F 149 PHE 0.015 0.001 PHE F 8 TRP 0.009 0.001 TRP E 103 HIS 0.006 0.002 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 9696) covalent geometry : angle 0.51519 / 0.27 (12983) SS BOND : bond 0.00285 / 0.15 ( 4) SS BOND : angle 0.84332 / 0.50 ( 8) hydrogen bonds : bond 0.04447 / 2.91 ( 738) hydrogen bonds : angle 3.43657 / 2.45 ( 2193) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.7845 (mtm110) REVERT: B 585 MET cc_start: 0.8538 (mmt) cc_final: 0.7574 (mmt) REVERT: C 566 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6733 (pm20) REVERT: C 590 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.7947 (mtm110) REVERT: D 585 MET cc_start: 0.8782 (mmt) cc_final: 0.7750 (mmt) REVERT: E 94 ASN cc_start: 0.7822 (m-40) cc_final: 0.7550 (m-40) REVERT: F 88 TRP cc_start: 0.5709 (m-10) cc_final: 0.5276 (m100) REVERT: F 94 ASN cc_start: 0.7739 (m-40) cc_final: 0.7481 (m-40) REVERT: H 23 LEU cc_start: 0.6194 (tp) cc_final: 0.5944 (mt) REVERT: H 88 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7314 (mtm-85) REVERT: H 122 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6996 (tpp80) REVERT: H 200 SER cc_start: 0.8039 (t) cc_final: 0.7789 (p) outliers start: 24 outliers final: 16 residues processed: 113 average time/residue: 0.5797 time to fit residues: 70.3855 Evaluate side-chains 112 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 122 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.0070 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150123 restraints weight = 9652.739| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.87 r_work: 0.3486 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9700 Z= 0.121 Angle : 0.449 7.604 12991 Z= 0.234 Chirality : 0.035 0.128 1447 Planarity : 0.003 0.035 1508 Dihedral : 14.198 144.067 1740 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.53 % Allowed : 11.24 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.25), residues: 1087 helix: 3.08 (0.16), residues: 885 sheet: -3.85 (0.74), residues: 20 loop : -0.99 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 541 TYR 0.025 0.001 TYR F 149 PHE 0.011 0.001 PHE B 531 TRP 0.008 0.001 TRP G 203 HIS 0.006 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9696) covalent geometry : angle 0.44875 / 0.23 (12983) SS BOND : bond 0.00228 / 0.12 ( 4) SS BOND : angle 0.80306 / 0.54 ( 8) hydrogen bonds : bond 0.04030 / 2.64 ( 738) hydrogen bonds : angle 3.29957 / 2.35 ( 2193) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.7967 (mtm110) REVERT: B 585 MET cc_start: 0.8610 (mmt) cc_final: 0.7768 (mmt) REVERT: C 566 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6547 (pm20) REVERT: C 590 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8091 (mtm110) REVERT: D 585 MET cc_start: 0.8846 (mmt) cc_final: 0.7842 (mmt) REVERT: E 94 ASN cc_start: 0.7772 (m-40) cc_final: 0.7508 (m-40) REVERT: F 88 TRP cc_start: 0.5807 (m-10) cc_final: 0.5233 (m100) REVERT: F 94 ASN cc_start: 0.7740 (m-40) cc_final: 0.7474 (m-40) REVERT: G 152 LYS cc_start: 0.5760 (mmpt) cc_final: 0.5510 (mmmt) REVERT: H 23 LEU cc_start: 0.6172 (tp) cc_final: 0.5882 (mt) REVERT: H 88 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7471 (mtm-85) REVERT: H 200 SER cc_start: 0.8188 (t) cc_final: 0.7933 (p) outliers start: 14 outliers final: 14 residues processed: 102 average time/residue: 0.5320 time to fit residues: 58.4332 Evaluate side-chains 109 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.193309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149399 restraints weight = 9667.436| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.84 r_work: 0.3479 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9700 Z= 0.133 Angle : 0.466 8.093 12991 Z= 0.242 Chirality : 0.036 0.144 1447 Planarity : 0.003 0.035 1508 Dihedral : 14.060 139.798 1740 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.75 % Allowed : 11.03 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.25), residues: 1087 helix: 3.10 (0.16), residues: 882 sheet: -5.66 (0.58), residues: 10 loop : -1.00 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 541 TYR 0.022 0.001 TYR F 149 PHE 0.012 0.001 PHE B 531 TRP 0.007 0.001 TRP G 203 HIS 0.006 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9696) covalent geometry : angle 0.46621 / 0.24 (12983) SS BOND : bond 0.00220 / 0.11 ( 4) SS BOND : angle 0.78719 / 0.53 ( 8) hydrogen bonds : bond 0.04075 / 2.66 ( 738) hydrogen bonds : angle 3.30391 / 2.36 ( 2193) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.7971 (mtm110) REVERT: A 807 LEU cc_start: 0.7970 (tm) cc_final: 0.7496 (tp) REVERT: C 541 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6961 (mmt-90) REVERT: C 566 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6704 (pm20) REVERT: C 590 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8079 (mtm110) REVERT: C 807 LEU cc_start: 0.8029 (tm) cc_final: 0.7555 (tp) REVERT: D 585 MET cc_start: 0.8840 (mmt) cc_final: 0.7843 (mmt) REVERT: E 94 ASN cc_start: 0.7768 (m-40) cc_final: 0.7494 (m-40) REVERT: F 88 TRP cc_start: 0.5868 (m-10) cc_final: 0.5301 (m100) REVERT: F 94 ASN cc_start: 0.7763 (m-40) cc_final: 0.7477 (m-40) REVERT: H 23 LEU cc_start: 0.6268 (tp) cc_final: 0.5942 (mt) REVERT: H 88 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7443 (mtm-85) REVERT: H 200 SER cc_start: 0.8187 (t) cc_final: 0.7929 (p) REVERT: H 218 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7705 (tp) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.5310 time to fit residues: 59.5145 Evaluate side-chains 111 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.193522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149741 restraints weight = 9653.998| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.84 r_work: 0.3483 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9700 Z= 0.132 Angle : 0.463 8.437 12991 Z= 0.240 Chirality : 0.036 0.162 1447 Planarity : 0.003 0.036 1508 Dihedral : 13.852 137.572 1740 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.86 % Allowed : 11.03 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.25), residues: 1087 helix: 3.12 (0.16), residues: 882 sheet: -5.66 (0.57), residues: 10 loop : -0.99 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.023 0.001 TYR F 149 PHE 0.011 0.001 PHE B 531 TRP 0.007 0.001 TRP G 203 HIS 0.006 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9696) covalent geometry : angle 0.46267 / 0.24 (12983) SS BOND : bond 0.00237 / 0.12 ( 4) SS BOND : angle 0.79642 / 0.52 ( 8) hydrogen bonds : bond 0.04038 / 2.64 ( 738) hydrogen bonds : angle 3.30617 / 2.36 ( 2193) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8002 (mtm110) REVERT: B 585 MET cc_start: 0.8614 (mmt) cc_final: 0.7835 (mmt) REVERT: C 566 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6684 (pm20) REVERT: C 590 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8109 (mtm110) REVERT: C 807 LEU cc_start: 0.8042 (tm) cc_final: 0.7558 (tp) REVERT: D 585 MET cc_start: 0.8838 (mmt) cc_final: 0.7834 (mmt) REVERT: E 94 ASN cc_start: 0.7773 (m-40) cc_final: 0.7505 (m-40) REVERT: F 94 ASN cc_start: 0.7763 (m-40) cc_final: 0.7480 (m-40) REVERT: H 23 LEU cc_start: 0.6290 (tp) cc_final: 0.5966 (mt) REVERT: H 88 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: H 200 SER cc_start: 0.8171 (t) cc_final: 0.7910 (p) REVERT: H 218 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7757 (tp) outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 0.5251 time to fit residues: 60.7224 Evaluate side-chains 112 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150097 restraints weight = 9571.748| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.85 r_work: 0.3490 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9700 Z= 0.127 Angle : 0.461 8.282 12991 Z= 0.240 Chirality : 0.036 0.138 1447 Planarity : 0.003 0.035 1508 Dihedral : 13.710 135.623 1740 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.53 % Allowed : 11.35 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.25), residues: 1087 helix: 3.15 (0.16), residues: 882 sheet: -5.66 (0.57), residues: 10 loop : -0.98 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.021 0.001 TYR G 226 PHE 0.009 0.001 PHE D 531 TRP 0.007 0.001 TRP G 203 HIS 0.006 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9696) covalent geometry : angle 0.46065 / 0.24 (12983) SS BOND : bond 0.00226 / 0.12 ( 4) SS BOND : angle 0.78262 / 0.53 ( 8) hydrogen bonds : bond 0.03993 / 2.61 ( 738) hydrogen bonds : angle 3.29259 / 2.36 ( 2193) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3300.27 seconds wall clock time: 57 minutes 1.53 seconds (3421.53 seconds total)