Starting phenix.real_space_refine on Tue Aug 4 17:14:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hl_75695/08_2026/11hl_75695_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hl_75695/08_2026/11hl_75695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11hl_75695/08_2026/11hl_75695_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hl_75695/08_2026/11hl_75695_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11hl_75695/08_2026/11hl_75695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hl_75695/08_2026/11hl_75695.map" } resolution = 2.8 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= 0.065 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3237 2.51 5 N 879 2.21 5 O 975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5118 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1640 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Restraints were copied for chains: B, C Time building chain proxies: 1.22, per 1000 atoms: 0.24 Number of scatterers: 5118 At special positions: 0 Unit cell: (71.294, 68.807, 130.153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 975 8.00 N 879 7.00 C 3237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1738 " - pdb=" SG CYS A1760 " distance=2.04 Simple disulfide: pdb=" SG CYS A1743 " - pdb=" SG CYS A1749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1048 " - pdb=" SG CYS B1059 " distance=2.01 Simple disulfide: pdb=" SG CYS C1048 " - pdb=" SG CYS C1059 " distance=2.01 Simple disulfide: pdb=" SG CYS B1738 " - pdb=" SG CYS B1760 " distance=2.04 Simple disulfide: pdb=" SG CYS C1738 " - pdb=" SG CYS C1760 " distance=2.04 Simple disulfide: pdb=" SG CYS B1743 " - pdb=" SG CYS B1749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1743 " - pdb=" SG CYS C1749 " 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 Links applied NAG-ASN " NAG A1401 " - " ASN A1709 " " NAG A1402 " - " ASN A1074 " " NAG A1403 " - " ASN A1098 " " NAG A1404 " - " ASN A1717 " " NAG B1401 " - " ASN B1709 " " NAG B1402 " - " ASN B1090 " " NAG B1403 " - " ASN B1114 " " NAG B1404 " - " ASN B1717 " " NAG C1401 " - " ASN C1709 " " NAG C1402 " - " ASN C1090 " " NAG C1403 " - " ASN C1114 " " NAG C1404 " - " ASN C1717 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 175.9 milliseconds 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1278 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 40.6% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 971 through 1032 removed outlier: 3.607A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1743 Processing helix chain 'A' and resid 1746 through 1754 Processing helix chain 'A' and resid 1755 through 1757 No H-bonds generated for 'chain 'A' and resid 1755 through 1757' Processing helix chain 'A' and resid 1758 through 1768 removed outlier: 4.128A pdb=" N GLN A1762 " --> pdb=" O SER A1758 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1048 removed outlier: 3.607A pdb=" N SER B1019 " --> pdb=" O GLY B1015 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B1022 " --> pdb=" O GLN B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1737 through 1743 Processing helix chain 'B' and resid 1746 through 1754 Processing helix chain 'B' and resid 1755 through 1757 No H-bonds generated for 'chain 'B' and resid 1755 through 1757' Processing helix chain 'B' and resid 1758 through 1768 removed outlier: 4.127A pdb=" N GLN B1762 " --> pdb=" O SER B1758 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1048 removed outlier: 3.607A pdb=" N SER C1019 " --> pdb=" O GLY C1015 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C1022 " --> pdb=" O GLN C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1737 through 1743 Processing helix chain 'C' and resid 1746 through 1754 Processing helix chain 'C' and resid 1755 through 1757 No H-bonds generated for 'chain 'C' and resid 1755 through 1757' Processing helix chain 'C' and resid 1758 through 1768 removed outlier: 4.128A pdb=" N GLN C1762 " --> pdb=" O SER C1758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1047 through 1056 removed outlier: 5.598A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1047 through 1056 removed outlier: 5.598A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN A1717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU A1072 " --> pdb=" O PRO A1715 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN A1074 " --> pdb=" O ALA A1713 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A1713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A1076 " --> pdb=" O SER A1711 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A1711 " --> pdb=" O THR A1076 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AA4, first strand: chain 'B' and resid 1063 through 1072 removed outlier: 5.597A pdb=" N HIS B1064 " --> pdb=" O TYR B1083 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR B1083 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B1092 " --> pdb=" O SER B1113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1063 through 1072 removed outlier: 5.597A pdb=" N HIS B1064 " --> pdb=" O TYR B1083 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR B1083 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN B1717 " --> pdb=" O ALA B1086 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B1088 " --> pdb=" O PRO B1715 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN B1090 " --> pdb=" O ALA B1713 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B1713 " --> pdb=" O ASN B1090 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B1092 " --> pdb=" O SER B1711 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER B1711 " --> pdb=" O THR B1092 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AA7, first strand: chain 'C' and resid 1063 through 1072 removed outlier: 5.598A pdb=" N HIS C1064 " --> pdb=" O TYR C1083 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR C1083 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR C1092 " --> pdb=" O SER C1113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1063 through 1072 removed outlier: 5.598A pdb=" N HIS C1064 " --> pdb=" O TYR C1083 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR C1083 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN C1717 " --> pdb=" O ALA C1086 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU C1088 " --> pdb=" O PRO C1715 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN C1090 " --> pdb=" O ALA C1713 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA C1713 " --> pdb=" O ASN C1090 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C1092 " --> pdb=" O SER C1711 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER C1711 " --> pdb=" O THR C1092 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1104 through 1106 322 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.49 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 872 1.31 - 1.44: 1327 1.44 - 1.56: 2940 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 5175 Sorted by residual: bond pdb=" NE ARG C1123 " pdb=" CZ ARG C1123 " ideal model delta sigma weight residual 1.326 1.368 -0.042 1.10e-02 8.26e+03 1.43e+01 bond pdb=" NE ARG A1107 " pdb=" CZ ARG A1107 " ideal model delta sigma weight residual 1.326 1.368 -0.042 1.10e-02 8.26e+03 1.43e+01 bond pdb=" C ASN A1709 " pdb=" O ASN A1709 " ideal model delta sigma weight residual 1.235 1.190 0.046 1.21e-02 6.83e+03 1.42e+01 bond pdb=" C ASN B1709 " pdb=" O ASN B1709 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.21e-02 6.83e+03 1.41e+01 bond pdb=" NE ARG B1123 " pdb=" CZ ARG B1123 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.40e+01 ... (remaining 5170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 6076 1.57 - 3.13: 814 3.13 - 4.70: 103 4.70 - 6.27: 42 6.27 - 7.83: 24 Bond angle restraints: 7059 Sorted by residual: angle pdb=" C GLU B1127 " pdb=" N PRO B1128 " pdb=" CA PRO B1128 " ideal model delta sigma weight residual 119.76 127.59 -7.83 1.03e+00 9.43e-01 5.78e+01 angle pdb=" C GLU A1111 " pdb=" N PRO A1112 " pdb=" CA PRO A1112 " ideal model delta sigma weight residual 119.76 127.59 -7.83 1.03e+00 9.43e-01 5.78e+01 angle pdb=" C GLU C1127 " pdb=" N PRO C1128 " pdb=" CA PRO C1128 " ideal model delta sigma weight residual 119.76 127.57 -7.81 1.03e+00 9.43e-01 5.74e+01 angle pdb=" C PHE C1105 " pdb=" N PRO C1106 " pdb=" CA PRO C1106 " ideal model delta sigma weight residual 119.85 126.58 -6.73 1.01e+00 9.80e-01 4.45e+01 angle pdb=" C PHE B1105 " pdb=" N PRO B1106 " pdb=" CA PRO B1106 " ideal model delta sigma weight residual 119.85 126.57 -6.72 1.01e+00 9.80e-01 4.43e+01 ... (remaining 7054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 3069 15.05 - 30.11: 132 30.11 - 45.16: 18 45.16 - 60.22: 15 60.22 - 75.27: 9 Dihedral angle restraints: 3243 sinusoidal: 1278 harmonic: 1965 Sorted by residual: dihedral pdb=" N ASN A1717 " pdb=" CA ASN A1717 " pdb=" CB ASN A1717 " pdb=" CG ASN A1717 " ideal model delta sinusoidal sigma weight residual -60.00 -105.15 45.15 3 1.50e+01 4.44e-03 8.12e+00 dihedral pdb=" N ASN B1717 " pdb=" CA ASN B1717 " pdb=" CB ASN B1717 " pdb=" CG ASN B1717 " ideal model delta sinusoidal sigma weight residual -60.00 -105.15 45.15 3 1.50e+01 4.44e-03 8.12e+00 dihedral pdb=" N ASN C1717 " pdb=" CA ASN C1717 " pdb=" CB ASN C1717 " pdb=" CG ASN C1717 " ideal model delta sinusoidal sigma weight residual -60.00 -105.14 45.14 3 1.50e+01 4.44e-03 8.12e+00 ... (remaining 3240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 620 0.060 - 0.120: 203 0.120 - 0.180: 43 0.180 - 0.240: 1 0.240 - 0.299: 15 Chirality restraints: 882 Sorted by residual: chirality pdb=" C1 NAG C1404 " pdb=" ND2 ASN C1717 " pdb=" C2 NAG C1404 " pdb=" O5 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B1709 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG A1401 " pdb=" ND2 ASN A1709 " pdb=" C2 NAG A1401 " pdb=" O5 NAG A1401 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 879 not shown) Planarity restraints: 912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C1137 " -0.040 2.00e-02 2.50e+03 2.50e-02 1.09e+01 pdb=" CG PHE C1137 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C1137 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C1137 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE C1137 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C1137 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE C1137 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1137 " 0.040 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE B1137 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE B1137 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B1137 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE B1137 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B1137 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B1137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1121 " 0.039 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE A1121 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A1121 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A1121 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE A1121 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A1121 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A1121 " 0.017 2.00e-02 2.50e+03 ... (remaining 909 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2044 2.90 - 3.40: 4962 3.40 - 3.90: 8817 3.90 - 4.40: 9995 4.40 - 4.90: 16373 Nonbonded interactions: 42191 Sorted by model distance: nonbonded pdb=" OG1 THR C1025 " pdb=" O HOH C1501 " model vdw 2.402 3.040 nonbonded pdb=" OG1 THR B1025 " pdb=" O HOH B1501 " model vdw 2.402 3.040 nonbonded pdb=" OG1 THR A1009 " pdb=" O HOH A1501 " model vdw 2.402 3.040 nonbonded pdb=" OG1 THR B1025 " pdb=" O HOH C1501 " model vdw 2.436 3.040 nonbonded pdb=" OG1 THR A1009 " pdb=" O HOH B1501 " model vdw 2.436 3.040 ... (remaining 42186 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.930 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.012 0.072 5196 Z= 0.715 Angle : 1.239 7.833 7113 Z= 0.850 Chirality : 0.070 0.299 882 Planarity : 0.006 0.029 900 Dihedral : 10.728 75.270 1938 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.30), residues: 657 helix: 1.44 (0.28), residues: 261 sheet: 1.40 (0.44), residues: 111 loop : -0.45 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1123 TYR 0.036 0.006 TYR C1083 PHE 0.040 0.006 PHE C1137 TRP 0.012 0.005 TRP B1118 HIS 0.005 0.002 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.01193 / 0.72 ( 5175) covalent geometry : angle 1.23537 / 0.85 ( 7059) SS BOND : bond 0.01199 / 0.83 ( 9) SS BOND : angle 1.26573 / 0.80 ( 18) hydrogen bonds : bond 0.18234 / 12.58 ( 298) hydrogen bonds : angle 7.78533 / 5.65 ( 930) link_NAG-ASN : bond 0.00355 / 0.27 ( 12) link_NAG-ASN : angle 1.84874 / 1.44 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1106 GLN cc_start: 0.8258 (pt0) cc_final: 0.7981 (pt0) REVERT: A 1108 ASN cc_start: 0.8542 (p0) cc_final: 0.8272 (p0) REVERT: A 1738 CYS cc_start: 0.6402 (m) cc_final: 0.6176 (m) REVERT: B 1122 GLN cc_start: 0.8235 (pt0) cc_final: 0.7750 (pt0) REVERT: B 1738 CYS cc_start: 0.6443 (m) cc_final: 0.6156 (m) REVERT: C 1122 GLN cc_start: 0.8273 (pt0) cc_final: 0.7972 (pt0) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3296 time to fit residues: 36.7657 Evaluate side-chains 62 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN A1048 HIS A1106 GLN A1119 ASN B1039 ASN B1064 HIS B1122 GLN C1039 ASN C1064 HIS C1122 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116898 restraints weight = 5608.085| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.73 r_work: 0.3271 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5196 Z= 0.146 Angle : 0.493 3.532 7113 Z= 0.273 Chirality : 0.042 0.153 882 Planarity : 0.004 0.026 900 Dihedral : 4.118 14.749 966 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.41 % Allowed : 6.71 % Favored : 87.88 % 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: 1.89 (0.32), residues: 657 helix: 3.03 (0.30), residues: 258 sheet: 1.35 (0.44), residues: 111 loop : -0.49 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1011 TYR 0.014 0.001 TYR B1083 PHE 0.013 0.002 PHE A1121 TRP 0.004 0.001 TRP A1102 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 5175) covalent geometry : angle 0.48667 / 0.27 ( 7059) SS BOND : bond 0.00310 / 0.21 ( 9) SS BOND : angle 0.64727 / 0.43 ( 18) hydrogen bonds : bond 0.06091 / 4.33 ( 298) hydrogen bonds : angle 5.09549 / 3.71 ( 930) link_NAG-ASN : bond 0.00441 / 0.34 ( 12) link_NAG-ASN : angle 1.13812 / 0.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1106 GLN cc_start: 0.8221 (pt0) cc_final: 0.7727 (pt0) REVERT: B 1122 GLN cc_start: 0.8229 (pt0) cc_final: 0.7685 (pt0) REVERT: C 1054 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (mttm) REVERT: C 1122 GLN cc_start: 0.8326 (pt0) cc_final: 0.7963 (pt0) outliers start: 25 outliers final: 3 residues processed: 90 average time/residue: 0.3552 time to fit residues: 33.6438 Evaluate side-chains 65 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain C residue 1054 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1039 ASN C1039 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116142 restraints weight = 5605.504| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.75 r_work: 0.3244 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5196 Z= 0.132 Angle : 0.448 3.269 7113 Z= 0.247 Chirality : 0.041 0.147 882 Planarity : 0.004 0.036 900 Dihedral : 3.905 15.548 966 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.68 % Allowed : 10.61 % Favored : 85.71 % 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: 2.07 (0.31), residues: 657 helix: 3.33 (0.30), residues: 258 sheet: 1.04 (0.41), residues: 126 loop : -0.45 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1123 TYR 0.013 0.001 TYR C1083 PHE 0.010 0.001 PHE C1137 TRP 0.004 0.001 TRP B1118 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 5175) covalent geometry : angle 0.44195 / 0.25 ( 7059) SS BOND : bond 0.00258 / 0.17 ( 9) SS BOND : angle 0.69601 / 0.45 ( 18) hydrogen bonds : bond 0.05604 / 3.99 ( 298) hydrogen bonds : angle 4.87442 / 3.55 ( 930) link_NAG-ASN : bond 0.00306 / 0.23 ( 12) link_NAG-ASN : angle 1.09211 / 0.84 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1045 MET cc_start: 0.8469 (tpt) cc_final: 0.8180 (tpt) REVERT: B 1122 GLN cc_start: 0.8192 (pt0) cc_final: 0.7740 (pt0) REVERT: C 1122 GLN cc_start: 0.8224 (pt0) cc_final: 0.7829 (pt0) REVERT: C 1738 CYS cc_start: 0.7517 (m) cc_final: 0.7154 (m) outliers start: 17 outliers final: 8 residues processed: 82 average time/residue: 0.4149 time to fit residues: 35.6342 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain B residue 1720 ILE Chi-restraints excluded: chain C residue 1061 LYS Chi-restraints excluded: chain C residue 1079 LEU Chi-restraints excluded: chain C residue 1731 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN A1119 ASN B1039 ASN C1018 GLN C1039 ASN C1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113351 restraints weight = 5707.259| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.77 r_work: 0.3215 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5196 Z= 0.168 Angle : 0.479 3.438 7113 Z= 0.260 Chirality : 0.042 0.155 882 Planarity : 0.004 0.040 900 Dihedral : 4.112 16.776 966 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.33 % Allowed : 10.39 % Favored : 85.28 % 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: 1.87 (0.31), residues: 657 helix: 3.10 (0.30), residues: 258 sheet: 1.19 (0.40), residues: 132 loop : -0.68 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1123 TYR 0.014 0.001 TYR B1083 PHE 0.009 0.001 PHE C1137 TRP 0.005 0.001 TRP C1118 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 5175) covalent geometry : angle 0.47313 / 0.26 ( 7059) SS BOND : bond 0.00341 / 0.23 ( 9) SS BOND : angle 0.64377 / 0.39 ( 18) hydrogen bonds : bond 0.06057 / 4.33 ( 298) hydrogen bonds : angle 4.92869 / 3.59 ( 930) link_NAG-ASN : bond 0.00287 / 0.21 ( 12) link_NAG-ASN : angle 1.13574 / 0.87 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1106 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: B 1122 GLN cc_start: 0.8190 (pt0) cc_final: 0.7762 (pt0) REVERT: C 1054 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8425 (mttm) REVERT: C 1122 GLN cc_start: 0.8192 (pt0) cc_final: 0.7613 (pt0) outliers start: 20 outliers final: 9 residues processed: 85 average time/residue: 0.3996 time to fit residues: 35.5487 Evaluate side-chains 84 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1720 ILE Chi-restraints excluded: chain C residue 1054 LYS Chi-restraints excluded: chain C residue 1079 LEU Chi-restraints excluded: chain C residue 1127 GLU Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN A1119 ASN B1039 ASN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114244 restraints weight = 5742.502| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.75 r_work: 0.3222 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5196 Z= 0.131 Angle : 0.437 3.299 7113 Z= 0.239 Chirality : 0.041 0.146 882 Planarity : 0.004 0.037 900 Dihedral : 3.949 15.892 966 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.90 % Allowed : 11.47 % Favored : 84.63 % 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: 1.93 (0.31), residues: 657 helix: 3.23 (0.30), residues: 258 sheet: 0.93 (0.42), residues: 128 loop : -0.53 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1123 TYR 0.013 0.001 TYR B1083 PHE 0.010 0.001 PHE C1137 TRP 0.007 0.001 TRP B1118 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 5175) covalent geometry : angle 0.43051 / 0.24 ( 7059) SS BOND : bond 0.00314 / 0.20 ( 9) SS BOND : angle 0.68514 / 0.43 ( 18) hydrogen bonds : bond 0.05514 / 3.94 ( 298) hydrogen bonds : angle 4.75427 / 3.46 ( 930) link_NAG-ASN : bond 0.00273 / 0.21 ( 12) link_NAG-ASN : angle 1.08253 / 0.83 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1045 MET cc_start: 0.8446 (tpt) cc_final: 0.8186 (tpt) REVERT: B 1122 GLN cc_start: 0.8145 (pt0) cc_final: 0.7687 (pt0) REVERT: C 1054 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8422 (mttm) REVERT: C 1122 GLN cc_start: 0.8102 (pt0) cc_final: 0.7754 (pt0) outliers start: 18 outliers final: 8 residues processed: 87 average time/residue: 0.4073 time to fit residues: 37.0707 Evaluate side-chains 86 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain C residue 1054 LYS Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1731 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN A1119 ASN B1039 ASN C1039 ASN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113685 restraints weight = 5682.717| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.76 r_work: 0.3218 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5196 Z= 0.145 Angle : 0.446 3.305 7113 Z= 0.244 Chirality : 0.041 0.145 882 Planarity : 0.004 0.036 900 Dihedral : 3.970 15.571 966 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.46 % Allowed : 11.69 % Favored : 84.85 % 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: 1.88 (0.31), residues: 657 helix: 3.20 (0.29), residues: 258 sheet: 0.94 (0.41), residues: 132 loop : -0.61 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1039 TYR 0.013 0.001 TYR B1083 PHE 0.009 0.001 PHE A1121 TRP 0.006 0.001 TRP B1118 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5175) covalent geometry : angle 0.43879 / 0.24 ( 7059) SS BOND : bond 0.00275 / 0.19 ( 9) SS BOND : angle 0.72938 / 0.45 ( 18) hydrogen bonds : bond 0.05691 / 4.06 ( 298) hydrogen bonds : angle 4.76230 / 3.46 ( 930) link_NAG-ASN : bond 0.00272 / 0.21 ( 12) link_NAG-ASN : angle 1.11989 / 0.84 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1106 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: B 1122 GLN cc_start: 0.8112 (pt0) cc_final: 0.7625 (pt0) REVERT: C 1045 MET cc_start: 0.8512 (tpt) cc_final: 0.8255 (tpt) REVERT: C 1054 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8433 (mttm) REVERT: C 1122 GLN cc_start: 0.8130 (pt0) cc_final: 0.7788 (pt0) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.4379 time to fit residues: 39.4957 Evaluate side-chains 83 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain C residue 1054 LYS Chi-restraints excluded: chain C residue 1061 LYS Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1731 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN A1119 ASN B1039 ASN B1751 ASN C1039 ASN C1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113562 restraints weight = 5669.538| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.76 r_work: 0.3204 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5196 Z= 0.144 Angle : 0.445 3.297 7113 Z= 0.243 Chirality : 0.041 0.144 882 Planarity : 0.004 0.037 900 Dihedral : 3.972 15.499 966 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.25 % Allowed : 12.55 % Favored : 84.20 % 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: 1.84 (0.31), residues: 657 helix: 3.20 (0.29), residues: 258 sheet: 0.77 (0.42), residues: 128 loop : -0.55 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1039 TYR 0.013 0.002 TYR B1083 PHE 0.009 0.001 PHE C1137 TRP 0.007 0.001 TRP B1118 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 5175) covalent geometry : angle 0.43769 / 0.24 ( 7059) SS BOND : bond 0.00274 / 0.19 ( 9) SS BOND : angle 0.79092 / 0.49 ( 18) hydrogen bonds : bond 0.05699 / 4.06 ( 298) hydrogen bonds : angle 4.73226 / 3.44 ( 930) link_NAG-ASN : bond 0.00276 / 0.21 ( 12) link_NAG-ASN : angle 1.14220 / 0.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: A 1106 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: B 1045 MET cc_start: 0.8409 (tpt) cc_final: 0.8100 (tpt) REVERT: B 1122 GLN cc_start: 0.8133 (pt0) cc_final: 0.7831 (pt0) REVERT: C 1054 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8452 (mttm) REVERT: C 1122 GLN cc_start: 0.8124 (pt0) cc_final: 0.7778 (pt0) outliers start: 15 outliers final: 9 residues processed: 84 average time/residue: 0.3990 time to fit residues: 35.2110 Evaluate side-chains 88 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain C residue 1054 LYS Chi-restraints excluded: chain C residue 1061 LYS Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1731 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.0030 chunk 55 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN A1119 ASN A1751 ASN B1039 ASN B1751 ASN C1039 ASN C1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114186 restraints weight = 5651.183| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.73 r_work: 0.3229 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5196 Z= 0.126 Angle : 0.434 3.300 7113 Z= 0.237 Chirality : 0.041 0.145 882 Planarity : 0.004 0.036 900 Dihedral : 3.926 15.535 966 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.25 % Allowed : 12.55 % Favored : 84.20 % 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: 1.87 (0.31), residues: 657 helix: 3.28 (0.29), residues: 258 sheet: 0.69 (0.42), residues: 128 loop : -0.54 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1039 TYR 0.012 0.001 TYR C1707 PHE 0.009 0.001 PHE C1137 TRP 0.007 0.001 TRP C1118 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 5175) covalent geometry : angle 0.42670 / 0.24 ( 7059) SS BOND : bond 0.00226 / 0.15 ( 9) SS BOND : angle 0.78366 / 0.49 ( 18) hydrogen bonds : bond 0.05463 / 3.89 ( 298) hydrogen bonds : angle 4.65732 / 3.39 ( 930) link_NAG-ASN : bond 0.00383 / 0.29 ( 12) link_NAG-ASN : angle 1.13535 / 0.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8056 (ttmt) REVERT: A 1106 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: B 1122 GLN cc_start: 0.8095 (pt0) cc_final: 0.7724 (pt0) REVERT: C 1054 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8429 (mttm) REVERT: C 1122 GLN cc_start: 0.8087 (pt0) cc_final: 0.7731 (pt0) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.4044 time to fit residues: 34.8145 Evaluate side-chains 87 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain C residue 1054 LYS Chi-restraints excluded: chain C residue 1061 LYS Chi-restraints excluded: chain C residue 1079 LEU Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1731 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN A1119 ASN A1751 ASN B1039 ASN B1104 HIS B1751 ASN C1039 ASN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113924 restraints weight = 5663.449| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.74 r_work: 0.3219 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5196 Z= 0.140 Angle : 0.444 3.286 7113 Z= 0.241 Chirality : 0.041 0.143 882 Planarity : 0.004 0.038 900 Dihedral : 3.965 15.696 966 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.81 % Allowed : 12.99 % Favored : 84.20 % 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: 1.81 (0.31), residues: 657 helix: 3.22 (0.29), residues: 258 sheet: 0.62 (0.42), residues: 128 loop : -0.56 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1039 TYR 0.013 0.002 TYR B1083 PHE 0.006 0.001 PHE B1137 TRP 0.006 0.001 TRP C1118 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 5175) covalent geometry : angle 0.43635 / 0.24 ( 7059) SS BOND : bond 0.00260 / 0.18 ( 9) SS BOND : angle 0.86309 / 0.53 ( 18) hydrogen bonds : bond 0.05634 / 4.02 ( 298) hydrogen bonds : angle 4.66660 / 3.40 ( 930) link_NAG-ASN : bond 0.00289 / 0.22 ( 12) link_NAG-ASN : angle 1.14872 / 0.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 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 1045 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8015 (ttmt) REVERT: A 1088 HIS cc_start: 0.8142 (m-70) cc_final: 0.7940 (m-70) REVERT: A 1106 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: B 1122 GLN cc_start: 0.8112 (pt0) cc_final: 0.7738 (pt0) REVERT: C 1054 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8444 (mttm) REVERT: C 1122 GLN cc_start: 0.8096 (pt0) cc_final: 0.7746 (pt0) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.4047 time to fit residues: 34.2364 Evaluate side-chains 83 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain C residue 1054 LYS Chi-restraints excluded: chain C residue 1079 LEU Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN A1119 ASN A1751 ASN B1039 ASN B1104 HIS B1751 ASN C1039 ASN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113250 restraints weight = 5728.020| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.75 r_work: 0.3206 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5196 Z= 0.156 Angle : 0.457 3.286 7113 Z= 0.247 Chirality : 0.041 0.140 882 Planarity : 0.004 0.040 900 Dihedral : 4.057 16.398 966 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.60 % Allowed : 13.20 % Favored : 84.20 % 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: 1.72 (0.31), residues: 657 helix: 3.15 (0.29), residues: 258 sheet: 0.57 (0.42), residues: 128 loop : -0.60 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1039 TYR 0.013 0.002 TYR C1707 PHE 0.007 0.001 PHE A1121 TRP 0.006 0.001 TRP C1118 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 5175) covalent geometry : angle 0.44838 / 0.25 ( 7059) SS BOND : bond 0.00311 / 0.21 ( 9) SS BOND : angle 0.87866 / 0.54 ( 18) hydrogen bonds : bond 0.05850 / 4.18 ( 298) hydrogen bonds : angle 4.69770 / 3.42 ( 930) link_NAG-ASN : bond 0.00286 / 0.22 ( 12) link_NAG-ASN : angle 1.17208 / 0.87 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8017 (ttmt) REVERT: A 1106 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: B 1122 GLN cc_start: 0.8110 (pt0) cc_final: 0.7665 (pt0) REVERT: C 1054 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8461 (mttm) REVERT: C 1122 GLN cc_start: 0.8092 (pt0) cc_final: 0.7743 (pt0) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.3980 time to fit residues: 34.9132 Evaluate side-chains 86 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1054 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain C residue 1054 LYS Chi-restraints excluded: chain C residue 1061 LYS Chi-restraints excluded: chain C residue 1079 LEU Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN A1088 HIS A1119 ASN A1751 ASN B1039 ASN B1104 HIS B1751 ASN C1039 ASN C1135 ASN C1751 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115206 restraints weight = 5731.233| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.64 r_work: 0.3239 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5196 Z= 0.123 Angle : 0.434 3.297 7113 Z= 0.236 Chirality : 0.041 0.144 882 Planarity : 0.004 0.039 900 Dihedral : 3.961 16.790 966 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.60 % Allowed : 13.20 % Favored : 84.20 % 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: 1.77 (0.31), residues: 657 helix: 3.26 (0.29), residues: 258 sheet: 0.50 (0.42), residues: 128 loop : -0.60 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1039 TYR 0.013 0.001 TYR C1707 PHE 0.007 0.001 PHE B1137 TRP 0.008 0.002 TRP C1118 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5175) covalent geometry : angle 0.42616 / 0.23 ( 7059) SS BOND : bond 0.00251 / 0.16 ( 9) SS BOND : angle 0.81621 / 0.51 ( 18) hydrogen bonds : bond 0.05434 / 3.87 ( 298) hydrogen bonds : angle 4.60132 / 3.35 ( 930) link_NAG-ASN : bond 0.00284 / 0.22 ( 12) link_NAG-ASN : angle 1.13380 / 0.84 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.22 seconds wall clock time: 33 minutes 23.01 seconds (2003.01 seconds total)