Starting phenix.real_space_refine on Sat Apr 4 22:51:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hn_75697/04_2026/11hn_75697_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hn_75697/04_2026/11hn_75697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11hn_75697/04_2026/11hn_75697_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hn_75697/04_2026/11hn_75697_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11hn_75697/04_2026/11hn_75697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hn_75697/04_2026/11hn_75697.map" } resolution = 2.7 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= 0.063 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 3255 2.51 5 N 885 2.21 5 O 1011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5178 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1649 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" 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: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Restraints were copied for chains: C, A Time building chain proxies: 1.07, per 1000 atoms: 0.21 Number of scatterers: 5178 At special positions: 0 Unit cell: (70.465, 71.294, 130.982, 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 1011 8.00 N 885 7.00 C 3255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B1048 " - pdb=" SG CYS B1059 " distance=2.01 Simple disulfide: pdb=" SG CYS B1738 " - pdb=" SG CYS B1760 " distance=2.04 Simple disulfide: pdb=" SG CYS B1743 " - pdb=" SG CYS B1749 " distance=2.11 Simple disulfide: pdb=" SG CYS C1048 " - pdb=" SG CYS C1059 " distance=2.01 Simple disulfide: pdb=" SG CYS A1048 " - pdb=" SG CYS A1059 " distance=2.01 Simple disulfide: pdb=" SG CYS C1738 " - pdb=" SG CYS C1760 " distance=2.04 Simple disulfide: pdb=" SG CYS A1738 " - pdb=" SG CYS A1760 " distance=2.04 Simple disulfide: pdb=" SG CYS C1743 " - pdb=" SG CYS C1749 " distance=2.11 Simple disulfide: pdb=" SG CYS A1743 " - pdb=" SG CYS A1749 " distance=2.11 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 A1090 " " NAG A1403 " - " ASN A1717 " " NAG A1404 " - " ASN A1114 " " NAG B1401 " - " ASN B1709 " " NAG B1402 " - " ASN B1090 " " NAG B1403 " - " ASN B1717 " " NAG B1404 " - " ASN B1114 " " NAG C1401 " - " ASN C1709 " " NAG C1402 " - " ASN C1090 " " NAG C1403 " - " ASN C1717 " " NAG C1404 " - " ASN C1114 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 281.8 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1284 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 44.8% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 987 through 1048 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1704 through 1708 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: 4.167A pdb=" N GLN B1762 " --> pdb=" O SER B1758 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1048 Processing helix chain 'C' and resid 1098 through 1102 Processing helix chain 'C' and resid 1704 through 1708 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: 4.167A pdb=" N GLN C1762 " --> pdb=" O SER C1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1048 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1704 through 1708 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: 4.167A pdb=" N GLN A1762 " --> pdb=" O SER A1758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1063 through 1072 removed outlier: 5.564A pdb=" N HIS B1064 " --> pdb=" O TYR B1083 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR B1083 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B1092 " --> pdb=" O SER B1113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1063 through 1072 removed outlier: 5.564A pdb=" N HIS B1064 " --> pdb=" O TYR B1083 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR B1083 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B1717 " --> pdb=" O ALA B1086 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU B1088 " --> pdb=" O PRO B1715 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN B1090 " --> pdb=" O ALA B1713 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B1713 " --> pdb=" O ASN B1090 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B1092 " --> pdb=" O SER B1711 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B1711 " --> pdb=" O THR B1092 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AA4, first strand: chain 'C' and resid 1063 through 1072 removed outlier: 5.564A pdb=" N HIS C1064 " --> pdb=" O TYR C1083 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR C1083 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR C1092 " --> pdb=" O SER C1113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1063 through 1072 removed outlier: 5.564A pdb=" N HIS C1064 " --> pdb=" O TYR C1083 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR C1083 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN C1717 " --> pdb=" O ALA C1086 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU C1088 " --> pdb=" O PRO C1715 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN C1090 " --> pdb=" O ALA C1713 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C1713 " --> pdb=" O ASN C1090 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C1092 " --> pdb=" O SER C1711 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER C1711 " --> pdb=" O THR C1092 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1104 through 1106 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1072 removed outlier: 5.564A pdb=" N HIS A1064 " --> pdb=" O TYR A1083 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A1083 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR A1092 " --> pdb=" O SER A1113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1063 through 1072 removed outlier: 5.564A pdb=" N HIS A1064 " --> pdb=" O TYR A1083 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A1083 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN A1717 " --> pdb=" O ALA A1086 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU A1088 " --> pdb=" O PRO A1715 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A1090 " --> pdb=" O ALA A1713 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA A1713 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A1092 " --> pdb=" O SER A1711 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER A1711 " --> pdb=" O THR A1092 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1104 through 1106 334 hydrogen bonds defined for protein. 939 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: 0.74 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1204 1.32 - 1.45: 1099 1.45 - 1.57: 2860 1.57 - 1.69: 9 1.69 - 1.81: 36 Bond restraints: 5208 Sorted by residual: bond pdb=" CD ARG B1030 " pdb=" NE ARG B1030 " ideal model delta sigma weight residual 1.458 1.405 0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" CD ARG A1030 " pdb=" NE ARG A1030 " ideal model delta sigma weight residual 1.458 1.405 0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" CD ARG C1030 " pdb=" NE ARG C1030 " ideal model delta sigma weight residual 1.458 1.405 0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" CG HIS A1104 " pdb=" CD2 HIS A1104 " ideal model delta sigma weight residual 1.354 1.316 0.038 1.10e-02 8.26e+03 1.21e+01 bond pdb=" CG HIS B1104 " pdb=" CD2 HIS B1104 " ideal model delta sigma weight residual 1.354 1.316 0.038 1.10e-02 8.26e+03 1.20e+01 ... (remaining 5203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 6261 1.59 - 3.17: 705 3.17 - 4.76: 80 4.76 - 6.34: 49 6.34 - 7.93: 18 Bond angle restraints: 7113 Sorted by residual: angle pdb=" C GLU B1127 " pdb=" N PRO B1128 " pdb=" CA PRO B1128 " ideal model delta sigma weight residual 119.76 127.69 -7.93 1.03e+00 9.43e-01 5.93e+01 angle pdb=" C GLU A1127 " pdb=" N PRO A1128 " pdb=" CA PRO A1128 " ideal model delta sigma weight residual 119.76 127.66 -7.90 1.03e+00 9.43e-01 5.89e+01 angle pdb=" C GLU C1127 " pdb=" N PRO C1128 " pdb=" CA PRO C1128 " ideal model delta sigma weight residual 119.76 127.65 -7.89 1.03e+00 9.43e-01 5.87e+01 angle pdb=" C ALA C1094 " pdb=" N PRO C1095 " pdb=" CA PRO C1095 " ideal model delta sigma weight residual 119.28 126.38 -7.10 1.10e+00 8.26e-01 4.17e+01 angle pdb=" C ALA A1094 " pdb=" N PRO A1095 " pdb=" CA PRO A1095 " ideal model delta sigma weight residual 119.28 126.37 -7.09 1.10e+00 8.26e-01 4.16e+01 ... (remaining 7108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.76: 3063 13.76 - 27.52: 144 27.52 - 41.28: 21 41.28 - 55.04: 15 55.04 - 68.81: 12 Dihedral angle restraints: 3255 sinusoidal: 1278 harmonic: 1977 Sorted by residual: dihedral pdb=" CG ARG B1107 " pdb=" CD ARG B1107 " pdb=" NE ARG B1107 " pdb=" CZ ARG B1107 " ideal model delta sinusoidal sigma weight residual 180.00 -138.77 -41.23 2 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CG ARG C1107 " pdb=" CD ARG C1107 " pdb=" NE ARG C1107 " pdb=" CZ ARG C1107 " ideal model delta sinusoidal sigma weight residual -180.00 -138.78 -41.22 2 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CG ARG A1107 " pdb=" CD ARG A1107 " pdb=" NE ARG A1107 " pdb=" CZ ARG A1107 " ideal model delta sinusoidal sigma weight residual -180.00 -138.78 -41.22 2 1.50e+01 4.44e-03 9.26e+00 ... (remaining 3252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 644 0.062 - 0.124: 196 0.124 - 0.186: 21 0.186 - 0.247: 15 0.247 - 0.309: 12 Chirality restraints: 888 Sorted by residual: chirality pdb=" C2 NAG A1404 " pdb=" C1 NAG A1404 " pdb=" C3 NAG A1404 " pdb=" N2 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.49 -2.80 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C2 NAG C1404 " pdb=" C1 NAG C1404 " pdb=" C3 NAG C1404 " pdb=" N2 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.49 -2.80 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2 NAG B1404 " pdb=" C1 NAG B1404 " pdb=" C3 NAG B1404 " pdb=" N2 NAG B1404 " both_signs ideal model delta sigma weight residual False -2.49 -2.80 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 885 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B1105 " -0.036 2.00e-02 2.50e+03 2.25e-02 8.82e+00 pdb=" CG PHE B1105 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B1105 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B1105 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B1105 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B1105 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B1105 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1105 " -0.036 2.00e-02 2.50e+03 2.24e-02 8.82e+00 pdb=" CG PHE A1105 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A1105 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A1105 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A1105 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A1105 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A1105 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C1105 " -0.036 2.00e-02 2.50e+03 2.24e-02 8.81e+00 pdb=" CG PHE C1105 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C1105 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C1105 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C1105 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C1105 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C1105 " -0.017 2.00e-02 2.50e+03 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 2838 2.99 - 3.47: 5059 3.47 - 3.95: 8997 3.95 - 4.42: 10418 4.42 - 4.90: 16164 Nonbonded interactions: 43476 Sorted by model distance: nonbonded pdb=" NZ LYS B1002 " pdb=" OE2 GLU B1006 " model vdw 2.518 3.120 nonbonded pdb=" NZ LYS C1002 " pdb=" OE2 GLU C1006 " model vdw 2.519 3.120 nonbonded pdb=" NZ LYS A1002 " pdb=" OE2 GLU A1006 " model vdw 2.519 3.120 nonbonded pdb=" O THR A1132 " pdb=" OD1 ASN A1135 " model vdw 2.541 3.040 nonbonded pdb=" O THR B1132 " pdb=" OD1 ASN B1135 " model vdw 2.541 3.040 ... (remaining 43471 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 'B' selection = chain 'C' selection = chain 'A' } 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: 22.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 0.082 5229 Z= 0.731 Angle : 1.178 7.929 7167 Z= 0.794 Chirality : 0.069 0.309 888 Planarity : 0.006 0.022 909 Dihedral : 10.375 68.805 1944 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.65 % Allowed : 0.65 % Favored : 98.71 % 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: 0.78 (0.29), residues: 666 helix: 1.46 (0.28), residues: 255 sheet: 0.79 (0.36), residues: 141 loop : -0.50 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1030 TYR 0.030 0.005 TYR B1083 PHE 0.037 0.006 PHE B1105 TRP 0.012 0.005 TRP B1118 HIS 0.011 0.003 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.01231 ( 5208) covalent geometry : angle 1.16810 ( 7113) SS BOND : bond 0.04838 ( 9) SS BOND : angle 2.12531 ( 18) hydrogen bonds : bond 0.19125 ( 310) hydrogen bonds : angle 7.76640 ( 939) link_NAG-ASN : bond 0.01915 ( 12) link_NAG-ASN : angle 2.06677 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.196 Fit side-chains REVERT: B 1054 LYS cc_start: 0.8262 (mttm) cc_final: 0.7794 (mmtt) REVERT: B 1717 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7675 (m-40) REVERT: C 1717 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7460 (m-40) REVERT: A 1050 LEU cc_start: 0.8417 (mt) cc_final: 0.8142 (mm) REVERT: A 1054 LYS cc_start: 0.8294 (mttm) cc_final: 0.7907 (mmtm) outliers start: 3 outliers final: 0 residues processed: 88 average time/residue: 0.5007 time to fit residues: 45.9754 Evaluate side-chains 54 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1717 ASN Chi-restraints excluded: chain C residue 1717 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1064 HIS B1099 HIS B1104 HIS B1751 ASN C 994 ASN C1064 HIS C1099 HIS C1104 HIS C1751 ASN A 994 ASN A1064 HIS A1099 HIS A1104 HIS A1751 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114079 restraints weight = 5995.796| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.47 r_work: 0.3225 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5229 Z= 0.183 Angle : 0.534 4.365 7167 Z= 0.289 Chirality : 0.042 0.162 888 Planarity : 0.004 0.029 909 Dihedral : 4.587 43.540 976 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.72 % Allowed : 6.67 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.30), residues: 666 helix: 2.93 (0.30), residues: 267 sheet: 0.59 (0.35), residues: 156 loop : -0.04 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1123 TYR 0.008 0.001 TYR C1083 PHE 0.019 0.002 PHE A1137 TRP 0.005 0.001 TRP C1118 HIS 0.005 0.002 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 5208) covalent geometry : angle 0.52176 ( 7113) SS BOND : bond 0.00211 ( 9) SS BOND : angle 0.81876 ( 18) hydrogen bonds : bond 0.07402 ( 310) hydrogen bonds : angle 5.12209 ( 939) link_NAG-ASN : bond 0.00262 ( 12) link_NAG-ASN : angle 1.61649 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8613 (mttm) cc_final: 0.8099 (mmtt) REVERT: C 1054 LYS cc_start: 0.8624 (mttp) cc_final: 0.8107 (mmtt) REVERT: A 1054 LYS cc_start: 0.8588 (mttm) cc_final: 0.8109 (mmtm) outliers start: 8 outliers final: 2 residues processed: 74 average time/residue: 0.4877 time to fit residues: 37.7419 Evaluate side-chains 64 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain C residue 1705 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 0.0270 chunk 23 optimal weight: 0.2980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.133066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114262 restraints weight = 5877.443| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.57 r_work: 0.3213 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5229 Z= 0.139 Angle : 0.461 3.561 7167 Z= 0.253 Chirality : 0.041 0.172 888 Planarity : 0.004 0.025 909 Dihedral : 3.812 15.417 972 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.51 % Allowed : 9.25 % Favored : 89.25 % 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: 2.22 (0.31), residues: 666 helix: 3.31 (0.30), residues: 267 sheet: 0.61 (0.35), residues: 156 loop : -0.05 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1123 TYR 0.010 0.001 TYR A1083 PHE 0.013 0.001 PHE A1137 TRP 0.005 0.001 TRP A1118 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5208) covalent geometry : angle 0.45024 ( 7113) SS BOND : bond 0.00305 ( 9) SS BOND : angle 0.69137 ( 18) hydrogen bonds : bond 0.06617 ( 310) hydrogen bonds : angle 4.84012 ( 939) link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 1.40224 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8616 (mttm) cc_final: 0.8075 (mmtt) REVERT: C 1054 LYS cc_start: 0.8628 (mttp) cc_final: 0.8108 (mmtt) REVERT: A 1054 LYS cc_start: 0.8602 (mttm) cc_final: 0.8116 (mmtm) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 0.5776 time to fit residues: 39.6640 Evaluate side-chains 64 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1705 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 994 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112071 restraints weight = 5813.515| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.55 r_work: 0.3182 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5229 Z= 0.170 Angle : 0.488 3.855 7167 Z= 0.265 Chirality : 0.042 0.159 888 Planarity : 0.004 0.030 909 Dihedral : 4.124 16.773 972 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.72 % Allowed : 9.68 % Favored : 88.60 % 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: 2.11 (0.31), residues: 666 helix: 3.26 (0.30), residues: 267 sheet: 0.54 (0.36), residues: 156 loop : -0.15 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1123 TYR 0.011 0.001 TYR A1083 PHE 0.012 0.002 PHE B1137 TRP 0.006 0.001 TRP A1118 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5208) covalent geometry : angle 0.47913 ( 7113) SS BOND : bond 0.00304 ( 9) SS BOND : angle 0.66221 ( 18) hydrogen bonds : bond 0.07018 ( 310) hydrogen bonds : angle 4.90364 ( 939) link_NAG-ASN : bond 0.00132 ( 12) link_NAG-ASN : angle 1.38010 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8640 (mttm) cc_final: 0.8149 (mmtt) REVERT: C 1002 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (tttt) REVERT: C 1054 LYS cc_start: 0.8655 (mttp) cc_final: 0.8137 (mmtt) REVERT: C 1725 GLU cc_start: 0.8825 (tt0) cc_final: 0.8600 (tt0) REVERT: A 1054 LYS cc_start: 0.8599 (mttm) cc_final: 0.8130 (mmtm) REVERT: A 1070 GLN cc_start: 0.8251 (mt0) cc_final: 0.7718 (mt0) outliers start: 8 outliers final: 3 residues processed: 72 average time/residue: 0.5642 time to fit residues: 42.4020 Evaluate side-chains 66 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1705 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.130421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111523 restraints weight = 5936.110| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.55 r_work: 0.3171 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5229 Z= 0.184 Angle : 0.499 4.469 7167 Z= 0.269 Chirality : 0.042 0.152 888 Planarity : 0.004 0.027 909 Dihedral : 4.292 17.517 972 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.86 % Allowed : 10.54 % Favored : 88.60 % 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: 666 helix: 3.23 (0.30), residues: 267 sheet: 0.58 (0.37), residues: 156 loop : -0.23 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1123 TYR 0.011 0.002 TYR C1083 PHE 0.012 0.002 PHE B1137 TRP 0.006 0.002 TRP A1118 HIS 0.005 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5208) covalent geometry : angle 0.49074 ( 7113) SS BOND : bond 0.00344 ( 9) SS BOND : angle 0.68317 ( 18) hydrogen bonds : bond 0.07124 ( 310) hydrogen bonds : angle 4.92362 ( 939) link_NAG-ASN : bond 0.00115 ( 12) link_NAG-ASN : angle 1.34439 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8654 (mttm) cc_final: 0.8147 (mmtt) REVERT: C 1054 LYS cc_start: 0.8658 (mttp) cc_final: 0.8161 (mmtt) REVERT: A 1054 LYS cc_start: 0.8673 (mttm) cc_final: 0.8178 (mmtm) REVERT: A 1070 GLN cc_start: 0.8229 (mt0) cc_final: 0.7715 (mt0) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.6180 time to fit residues: 41.1837 Evaluate side-chains 64 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1705 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 0.0030 chunk 43 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 36 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.1568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1021 GLN C1021 GLN A1021 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117458 restraints weight = 5934.106| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.55 r_work: 0.3266 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5229 Z= 0.104 Angle : 0.420 3.315 7167 Z= 0.228 Chirality : 0.041 0.162 888 Planarity : 0.003 0.028 909 Dihedral : 3.566 13.298 972 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.65 % Allowed : 10.75 % Favored : 88.60 % 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: 2.46 (0.31), residues: 666 helix: 4.01 (0.29), residues: 255 sheet: 0.74 (0.37), residues: 156 loop : -0.34 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1123 TYR 0.010 0.001 TYR C1083 PHE 0.009 0.001 PHE B1137 TRP 0.006 0.001 TRP A1118 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 5208) covalent geometry : angle 0.41123 ( 7113) SS BOND : bond 0.00110 ( 9) SS BOND : angle 0.68112 ( 18) hydrogen bonds : bond 0.05608 ( 310) hydrogen bonds : angle 4.43043 ( 939) link_NAG-ASN : bond 0.00234 ( 12) link_NAG-ASN : angle 1.21559 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8590 (mttm) cc_final: 0.8088 (mmtt) REVERT: C 1054 LYS cc_start: 0.8581 (mttp) cc_final: 0.8104 (mmtt) REVERT: C 1725 GLU cc_start: 0.8814 (tt0) cc_final: 0.8577 (tt0) REVERT: A 1054 LYS cc_start: 0.8580 (mttm) cc_final: 0.8105 (mmtm) REVERT: A 1070 GLN cc_start: 0.8169 (mt0) cc_final: 0.7781 (mt0) outliers start: 3 outliers final: 1 residues processed: 67 average time/residue: 0.6023 time to fit residues: 42.0209 Evaluate side-chains 63 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1705 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.130496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111427 restraints weight = 5939.197| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.57 r_work: 0.3164 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5229 Z= 0.197 Angle : 0.506 4.546 7167 Z= 0.271 Chirality : 0.043 0.150 888 Planarity : 0.004 0.030 909 Dihedral : 4.200 16.375 972 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.08 % Allowed : 10.75 % Favored : 88.17 % 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: 2.21 (0.31), residues: 666 helix: 3.76 (0.29), residues: 255 sheet: 0.60 (0.37), residues: 156 loop : -0.43 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.011 0.002 TYR A1083 PHE 0.012 0.002 PHE B1137 TRP 0.006 0.002 TRP A1118 HIS 0.006 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5208) covalent geometry : angle 0.49886 ( 7113) SS BOND : bond 0.00373 ( 9) SS BOND : angle 0.62127 ( 18) hydrogen bonds : bond 0.07222 ( 310) hydrogen bonds : angle 4.83564 ( 939) link_NAG-ASN : bond 0.00089 ( 12) link_NAG-ASN : angle 1.24651 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8657 (mttm) cc_final: 0.8181 (mmtm) REVERT: C 1054 LYS cc_start: 0.8677 (mttp) cc_final: 0.8203 (mmtt) REVERT: A 1054 LYS cc_start: 0.8672 (mttm) cc_final: 0.8187 (mmtm) REVERT: A 1070 GLN cc_start: 0.8219 (mt0) cc_final: 0.7756 (mt0) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.5739 time to fit residues: 40.0155 Evaluate side-chains 65 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1705 VAL Chi-restraints excluded: chain A residue 1705 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.130626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111832 restraints weight = 5876.538| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.55 r_work: 0.3171 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5229 Z= 0.186 Angle : 0.499 4.627 7167 Z= 0.267 Chirality : 0.043 0.147 888 Planarity : 0.004 0.028 909 Dihedral : 4.293 19.007 972 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.86 % Allowed : 10.75 % Favored : 88.39 % 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: 666 helix: 3.67 (0.29), residues: 255 sheet: 0.54 (0.37), residues: 156 loop : -0.54 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.011 0.002 TYR A1083 PHE 0.011 0.002 PHE A1137 TRP 0.006 0.002 TRP A1118 HIS 0.005 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5208) covalent geometry : angle 0.49216 ( 7113) SS BOND : bond 0.00324 ( 9) SS BOND : angle 0.65600 ( 18) hydrogen bonds : bond 0.07067 ( 310) hydrogen bonds : angle 4.82256 ( 939) link_NAG-ASN : bond 0.00076 ( 12) link_NAG-ASN : angle 1.25568 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8666 (mttm) cc_final: 0.8170 (mmtt) REVERT: C 1054 LYS cc_start: 0.8666 (mttp) cc_final: 0.8210 (mmtt) REVERT: A 1054 LYS cc_start: 0.8699 (mttm) cc_final: 0.8222 (mmtm) REVERT: A 1070 GLN cc_start: 0.8245 (mt0) cc_final: 0.7769 (mt0) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.5786 time to fit residues: 40.9269 Evaluate side-chains 66 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1705 VAL Chi-restraints excluded: chain A residue 1705 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.129949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111243 restraints weight = 5899.236| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.54 r_work: 0.3166 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5229 Z= 0.203 Angle : 0.518 4.962 7167 Z= 0.276 Chirality : 0.043 0.148 888 Planarity : 0.004 0.031 909 Dihedral : 4.434 20.955 972 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.29 % Allowed : 10.32 % Favored : 88.39 % 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: 1.99 (0.31), residues: 666 helix: 3.62 (0.29), residues: 255 sheet: 0.46 (0.37), residues: 156 loop : -0.57 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.011 0.002 TYR A1083 PHE 0.012 0.002 PHE B1137 TRP 0.006 0.002 TRP A1118 HIS 0.006 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 5208) covalent geometry : angle 0.51147 ( 7113) SS BOND : bond 0.00364 ( 9) SS BOND : angle 0.63375 ( 18) hydrogen bonds : bond 0.07315 ( 310) hydrogen bonds : angle 4.89321 ( 939) link_NAG-ASN : bond 0.00062 ( 12) link_NAG-ASN : angle 1.22076 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8676 (mttm) cc_final: 0.8192 (mmtt) REVERT: C 1002 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8414 (tttt) REVERT: C 1054 LYS cc_start: 0.8674 (mttp) cc_final: 0.8217 (mmtt) REVERT: A 1054 LYS cc_start: 0.8689 (mttm) cc_final: 0.8213 (mmtm) REVERT: A 1070 GLN cc_start: 0.8244 (mt0) cc_final: 0.7773 (mt0) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.5943 time to fit residues: 41.3616 Evaluate side-chains 69 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1705 VAL Chi-restraints excluded: chain A residue 1705 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 64 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.130087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111167 restraints weight = 5967.430| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.57 r_work: 0.3165 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5229 Z= 0.195 Angle : 0.510 5.045 7167 Z= 0.272 Chirality : 0.043 0.149 888 Planarity : 0.004 0.030 909 Dihedral : 4.370 20.523 972 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.29 % Allowed : 10.32 % Favored : 88.39 % 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: 1.97 (0.31), residues: 666 helix: 3.61 (0.29), residues: 255 sheet: 0.43 (0.38), residues: 156 loop : -0.57 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.011 0.002 TYR A1083 PHE 0.012 0.002 PHE B1137 TRP 0.006 0.002 TRP A1118 HIS 0.005 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5208) covalent geometry : angle 0.50380 ( 7113) SS BOND : bond 0.00345 ( 9) SS BOND : angle 0.62788 ( 18) hydrogen bonds : bond 0.07183 ( 310) hydrogen bonds : angle 4.86488 ( 939) link_NAG-ASN : bond 0.00071 ( 12) link_NAG-ASN : angle 1.19786 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1054 LYS cc_start: 0.8666 (mttm) cc_final: 0.8170 (mmtt) REVERT: C 1002 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8407 (tttt) REVERT: C 1054 LYS cc_start: 0.8668 (mttp) cc_final: 0.8206 (mmtt) REVERT: A 1054 LYS cc_start: 0.8693 (mttm) cc_final: 0.8212 (mmtm) REVERT: A 1070 GLN cc_start: 0.8233 (mt0) cc_final: 0.7756 (mt0) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.5756 time to fit residues: 40.6944 Evaluate side-chains 70 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1705 VAL Chi-restraints excluded: chain A residue 1705 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.130091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111882 restraints weight = 5924.132| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.48 r_work: 0.3166 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5229 Z= 0.196 Angle : 0.514 5.058 7167 Z= 0.274 Chirality : 0.043 0.152 888 Planarity : 0.004 0.030 909 Dihedral : 4.390 20.569 972 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.08 % Allowed : 10.75 % Favored : 88.17 % 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 (0.31), residues: 666 helix: 3.60 (0.29), residues: 255 sheet: 0.42 (0.38), residues: 156 loop : -0.58 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.011 0.002 TYR A1083 PHE 0.012 0.002 PHE B1137 TRP 0.006 0.002 TRP A1118 HIS 0.005 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 5208) covalent geometry : angle 0.50834 ( 7113) SS BOND : bond 0.00343 ( 9) SS BOND : angle 0.63439 ( 18) hydrogen bonds : bond 0.07219 ( 310) hydrogen bonds : angle 4.88298 ( 939) link_NAG-ASN : bond 0.00064 ( 12) link_NAG-ASN : angle 1.18684 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.41 seconds wall clock time: 36 minutes 46.24 seconds (2206.24 seconds total)