Starting phenix.real_space_refine on Tue Mar 3 14:51:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22xo_68756/03_2026/22xo_68756.cif Found real_map, /net/cci-nas-00/data/ceres_data/22xo_68756/03_2026/22xo_68756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22xo_68756/03_2026/22xo_68756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22xo_68756/03_2026/22xo_68756.map" model { file = "/net/cci-nas-00/data/ceres_data/22xo_68756/03_2026/22xo_68756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22xo_68756/03_2026/22xo_68756.cif" } resolution = 2.72 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= 0.002 sd= 0.029 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 40 5.16 5 C 3994 2.51 5 N 1042 2.21 5 O 1182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6258 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1644 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1485 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 174} Chain: "C" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1644 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1485 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 174} Time building chain proxies: 1.50, per 1000 atoms: 0.24 Number of scatterers: 6258 At special positions: 0 Unit cell: (81.37, 79.31, 79.31, 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 40 16.00 O 1182 8.00 N 1042 7.00 C 3994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 340.2 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 45.2% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 removed outlier: 3.952A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.782A pdb=" N ASP A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.501A pdb=" N TYR A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 207 through 222 Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.768A pdb=" N ASP B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 45 " --> pdb=" O GLU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 207 through 222 Processing helix chain 'C' and resid 12 through 25 Processing helix chain 'C' and resid 39 through 46 removed outlier: 3.901A pdb=" N ASP C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 129 through 143 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.621A pdb=" N ASN C 206 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 222 Processing helix chain 'D' and resid 39 through 58 removed outlier: 3.821A pdb=" N ASP D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Proline residue: D 48 - end of helix Processing helix chain 'D' and resid 69 through 79 removed outlier: 3.890A pdb=" N ALA D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 142 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 207 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 67 removed outlier: 6.317A pdb=" N LEU A 34 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ARG A 66 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE A 36 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU A 84 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR A 35 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL A 86 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 37 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 85 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 100 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 199 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN A 98 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TYR A 201 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ALA A 96 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 removed outlier: 4.134A pdb=" N TRP A 106 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 125 removed outlier: 8.108A pdb=" N LEU A 124 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 151 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 67 removed outlier: 9.062A pdb=" N LEU B 84 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR B 35 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N VAL B 86 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY B 37 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B 100 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 199 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN B 98 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR B 201 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ALA B 96 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 171 removed outlier: 4.002A pdb=" N TRP B 106 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 125 removed outlier: 8.167A pdb=" N LEU B 124 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 151 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 67 removed outlier: 6.391A pdb=" N LEU C 34 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARG C 66 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 36 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU C 84 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 100 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.968A pdb=" N TRP C 106 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 125 removed outlier: 8.257A pdb=" N LEU C 124 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL C 151 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 62 through 67 removed outlier: 4.086A pdb=" N LEU D 84 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG D 100 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU D 199 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN D 98 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR D 201 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA D 96 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 172 removed outlier: 3.956A pdb=" N TRP D 106 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 125 removed outlier: 8.267A pdb=" N LEU D 124 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL D 151 " --> pdb=" O LEU D 124 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 795 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: 0.87 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1929 1.34 - 1.46: 920 1.46 - 1.58: 3483 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 6402 Sorted by residual: bond pdb=" CB GLU C 118 " pdb=" CG GLU C 118 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" CA MET C 26 " pdb=" CB MET C 26 " ideal model delta sigma weight residual 1.531 1.546 -0.016 1.48e-02 4.57e+03 1.10e+00 bond pdb=" CA ILE C 144 " pdb=" C ILE C 144 " ideal model delta sigma weight residual 1.516 1.527 -0.011 1.11e-02 8.12e+03 9.95e-01 bond pdb=" C LEU C 155 " pdb=" N PRO C 156 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.28e-02 6.10e+03 9.81e-01 bond pdb=" CG MET A 73 " pdb=" SD MET A 73 " ideal model delta sigma weight residual 1.803 1.779 0.024 2.50e-02 1.60e+03 9.53e-01 ... (remaining 6397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 8546 2.01 - 4.03: 174 4.03 - 6.04: 26 6.04 - 8.05: 5 8.05 - 10.06: 3 Bond angle restraints: 8754 Sorted by residual: angle pdb=" CA MET C 26 " pdb=" CB MET C 26 " pdb=" CG MET C 26 " ideal model delta sigma weight residual 114.10 122.47 -8.37 2.00e+00 2.50e-01 1.75e+01 angle pdb=" N GLN C 31 " pdb=" CA GLN C 31 " pdb=" C GLN C 31 " ideal model delta sigma weight residual 110.35 115.41 -5.06 1.38e+00 5.25e-01 1.34e+01 angle pdb=" CB MET D 73 " pdb=" CG MET D 73 " pdb=" SD MET D 73 " ideal model delta sigma weight residual 112.70 102.64 10.06 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB GLU C 118 " pdb=" CG GLU C 118 " pdb=" CD GLU C 118 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.70e+00 3.46e-01 1.04e+01 angle pdb=" C ILE C 144 " pdb=" CA ILE C 144 " pdb=" CB ILE C 144 " ideal model delta sigma weight residual 109.33 112.49 -3.16 9.80e-01 1.04e+00 1.04e+01 ... (remaining 8749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.90: 3304 11.90 - 23.80: 417 23.80 - 35.70: 138 35.70 - 47.60: 55 47.60 - 59.50: 32 Dihedral angle restraints: 3946 sinusoidal: 1540 harmonic: 2406 Sorted by residual: dihedral pdb=" CA LEU C 30 " pdb=" C LEU C 30 " pdb=" N GLN C 31 " pdb=" CA GLN C 31 " ideal model delta harmonic sigma weight residual -180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA TYR A 72 " pdb=" C TYR A 72 " pdb=" N MET A 73 " pdb=" CA MET A 73 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA TYR B 72 " pdb=" C TYR B 72 " pdb=" N MET B 73 " pdb=" CA MET B 73 " ideal model delta harmonic sigma weight residual 180.00 -157.86 -22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 3943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 625 0.031 - 0.062: 264 0.062 - 0.093: 90 0.093 - 0.124: 44 0.124 - 0.155: 3 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CG LEU D 51 " pdb=" CB LEU D 51 " pdb=" CD1 LEU D 51 " pdb=" CD2 LEU D 51 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA VAL D 168 " pdb=" N VAL D 168 " pdb=" C VAL D 168 " pdb=" CB VAL D 168 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ASN D 52 " pdb=" N ASN D 52 " pdb=" C ASN D 52 " pdb=" CB ASN D 52 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1023 not shown) Planarity restraints: 1130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 118 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.71e+00 pdb=" CD GLU C 118 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU C 118 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU C 118 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 127 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO D 128 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 177 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO C 178 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.027 5.00e-02 4.00e+02 ... (remaining 1127 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 2458 2.92 - 3.42: 6151 3.42 - 3.91: 10495 3.91 - 4.41: 11073 4.41 - 4.90: 19298 Nonbonded interactions: 49475 Sorted by model distance: nonbonded pdb=" O PRO D 48 " pdb=" OD1 ASN D 52 " model vdw 2.428 3.040 nonbonded pdb=" N GLU C 118 " pdb=" OE1 GLU C 118 " model vdw 2.512 3.120 nonbonded pdb=" N MET C 26 " pdb=" O MET C 26 " model vdw 2.560 2.496 nonbonded pdb=" N TYR C 72 " pdb=" N MET C 73 " model vdw 2.603 2.560 nonbonded pdb=" N CYS B 108 " pdb=" O CYS B 108 " model vdw 2.613 2.496 ... (remaining 49470 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' and resid 32 through 223) selection = (chain 'B' and (resid 32 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 223)) selection = (chain 'C' and resid 32 through 223) selection = (chain 'D' and (resid 32 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 223)) } 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: 0.550 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.500 Find NCS groups from input model: 0.120 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 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 : 0.003 0.043 6402 Z= 0.139 Angle : 0.706 10.063 8754 Z= 0.372 Chirality : 0.042 0.155 1026 Planarity : 0.006 0.048 1130 Dihedral : 13.953 59.502 2382 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.00 % Favored : 97.88 % Rotamer: Outliers : 2.45 % Allowed : 17.15 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.15 (0.29), residues: 802 helix: 1.88 (0.30), residues: 276 sheet: 0.56 (0.43), residues: 149 loop : 0.10 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 53 TYR 0.010 0.001 TYR B 72 PHE 0.009 0.001 PHE C 27 TRP 0.007 0.001 TRP B 106 HIS 0.002 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6402) covalent geometry : angle 0.70577 ( 8754) hydrogen bonds : bond 0.15515 ( 294) hydrogen bonds : angle 5.74471 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6726 (mm-40) cc_final: 0.6203 (mm110) REVERT: B 132 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6231 (ptm160) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.3594 time to fit residues: 41.3377 Evaluate side-chains 107 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 200 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4983 r_free = 0.4983 target = 0.234722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.208069 restraints weight = 7757.535| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 2.56 r_work: 0.4607 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6402 Z= 0.163 Angle : 0.648 8.350 8754 Z= 0.316 Chirality : 0.043 0.189 1026 Planarity : 0.006 0.050 1130 Dihedral : 7.270 54.807 918 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.37 % Favored : 97.51 % Rotamer: Outliers : 4.18 % Allowed : 15.42 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.11 (0.30), residues: 802 helix: 1.67 (0.30), residues: 293 sheet: 0.44 (0.44), residues: 150 loop : 0.21 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 171 TYR 0.012 0.002 TYR B 72 PHE 0.013 0.001 PHE B 131 TRP 0.011 0.001 TRP A 106 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6402) covalent geometry : angle 0.64779 ( 8754) hydrogen bonds : bond 0.03519 ( 294) hydrogen bonds : angle 4.65077 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6539 (mm-40) cc_final: 0.6108 (mm110) REVERT: A 144 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5781 (pp) REVERT: B 144 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6077 (pt) outliers start: 29 outliers final: 11 residues processed: 102 average time/residue: 0.3557 time to fit residues: 39.0060 Evaluate side-chains 105 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 40 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.232763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.206506 restraints weight = 7663.185| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 2.49 r_work: 0.4598 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6402 Z= 0.155 Angle : 0.650 10.615 8754 Z= 0.313 Chirality : 0.044 0.248 1026 Planarity : 0.006 0.050 1130 Dihedral : 6.654 50.713 905 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.24 % Favored : 96.63 % Rotamer: Outliers : 4.47 % Allowed : 15.27 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.09 (0.29), residues: 802 helix: 1.82 (0.30), residues: 288 sheet: 0.41 (0.44), residues: 148 loop : 0.05 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.013 0.001 TYR B 72 PHE 0.012 0.002 PHE B 131 TRP 0.014 0.001 TRP D 106 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6402) covalent geometry : angle 0.64984 ( 8754) hydrogen bonds : bond 0.03403 ( 294) hydrogen bonds : angle 4.62706 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.4775 (OUTLIER) cc_final: 0.4506 (ppp) REVERT: A 115 GLN cc_start: 0.6533 (mm-40) cc_final: 0.6114 (mm110) REVERT: A 144 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5698 (pp) REVERT: B 144 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6163 (pt) outliers start: 31 outliers final: 10 residues processed: 107 average time/residue: 0.3658 time to fit residues: 41.9257 Evaluate side-chains 102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 77 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.232583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.206153 restraints weight = 7723.988| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.51 r_work: 0.4598 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6402 Z= 0.149 Angle : 0.643 10.448 8754 Z= 0.309 Chirality : 0.042 0.212 1026 Planarity : 0.006 0.047 1130 Dihedral : 6.294 43.795 902 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.90 % Allowed : 16.71 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.03 (0.29), residues: 802 helix: 1.92 (0.30), residues: 286 sheet: 0.24 (0.44), residues: 150 loop : -0.05 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.014 0.001 TYR C 58 PHE 0.032 0.002 PHE C 27 TRP 0.015 0.001 TRP D 106 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6402) covalent geometry : angle 0.64279 ( 8754) hydrogen bonds : bond 0.03191 ( 294) hydrogen bonds : angle 4.52354 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6539 (mm-40) cc_final: 0.6103 (mm110) REVERT: A 144 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5678 (pp) REVERT: B 123 VAL cc_start: 0.8020 (p) cc_final: 0.7769 (m) REVERT: B 144 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.5894 (pt) REVERT: C 20 GLU cc_start: 0.3088 (OUTLIER) cc_final: 0.2880 (tm-30) outliers start: 34 outliers final: 14 residues processed: 106 average time/residue: 0.3319 time to fit residues: 37.9027 Evaluate side-chains 104 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.230631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.203950 restraints weight = 7878.993| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 2.59 r_work: 0.4571 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6402 Z= 0.165 Angle : 0.662 10.392 8754 Z= 0.316 Chirality : 0.043 0.201 1026 Planarity : 0.006 0.049 1130 Dihedral : 6.321 44.172 902 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.32 % Allowed : 17.44 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.91 (0.29), residues: 802 helix: 1.91 (0.30), residues: 280 sheet: 0.25 (0.45), residues: 144 loop : -0.19 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 171 TYR 0.011 0.002 TYR B 107 PHE 0.022 0.002 PHE C 27 TRP 0.014 0.002 TRP D 106 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6402) covalent geometry : angle 0.66219 ( 8754) hydrogen bonds : bond 0.03250 ( 294) hydrogen bonds : angle 4.58191 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.4840 (tmt) cc_final: 0.4407 (tmt) REVERT: A 115 GLN cc_start: 0.6448 (mm-40) cc_final: 0.6032 (mm110) REVERT: A 144 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5547 (pp) REVERT: A 150 TYR cc_start: 0.7659 (t80) cc_final: 0.7422 (t80) REVERT: B 123 VAL cc_start: 0.8022 (p) cc_final: 0.7792 (m) REVERT: B 144 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.5893 (pt) REVERT: C 123 VAL cc_start: 0.8152 (p) cc_final: 0.7887 (m) outliers start: 30 outliers final: 19 residues processed: 108 average time/residue: 0.3453 time to fit residues: 40.1093 Evaluate side-chains 114 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4924 r_free = 0.4924 target = 0.228838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.202878 restraints weight = 7740.019| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 2.53 r_work: 0.4562 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6402 Z= 0.171 Angle : 0.664 10.542 8754 Z= 0.319 Chirality : 0.043 0.187 1026 Planarity : 0.006 0.048 1130 Dihedral : 6.361 46.908 902 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.19 % Allowed : 15.71 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.82 (0.29), residues: 802 helix: 1.87 (0.30), residues: 280 sheet: -0.02 (0.43), residues: 158 loop : -0.17 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.011 0.002 TYR C 58 PHE 0.032 0.002 PHE C 27 TRP 0.013 0.001 TRP D 106 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6402) covalent geometry : angle 0.66360 ( 8754) hydrogen bonds : bond 0.03337 ( 294) hydrogen bonds : angle 4.62231 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.4658 (tpt) REVERT: A 115 GLN cc_start: 0.6490 (mm-40) cc_final: 0.6020 (mm110) REVERT: A 144 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5520 (pp) REVERT: B 123 VAL cc_start: 0.8034 (p) cc_final: 0.7797 (m) REVERT: B 132 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5719 (ptm160) REVERT: B 144 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6011 (pt) outliers start: 36 outliers final: 19 residues processed: 114 average time/residue: 0.3144 time to fit residues: 38.7888 Evaluate side-chains 121 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 134 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.230160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.203915 restraints weight = 7654.756| |-----------------------------------------------------------------------------| r_work (start): 0.4689 rms_B_bonded: 2.47 r_work: 0.4578 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6402 Z= 0.173 Angle : 0.682 10.131 8754 Z= 0.327 Chirality : 0.043 0.185 1026 Planarity : 0.006 0.048 1130 Dihedral : 6.325 49.491 902 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.76 % Allowed : 16.71 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.77 (0.29), residues: 802 helix: 1.75 (0.30), residues: 282 sheet: -0.07 (0.43), residues: 156 loop : -0.12 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 171 TYR 0.020 0.002 TYR A 150 PHE 0.031 0.002 PHE C 27 TRP 0.013 0.001 TRP D 106 HIS 0.002 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6402) covalent geometry : angle 0.68217 ( 8754) hydrogen bonds : bond 0.03326 ( 294) hydrogen bonds : angle 4.68173 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.159 Fit side-chains REVERT: A 73 MET cc_start: 0.4913 (OUTLIER) cc_final: 0.4449 (tmt) REVERT: A 115 GLN cc_start: 0.6527 (mm-40) cc_final: 0.6070 (mm110) REVERT: A 132 ARG cc_start: 0.6223 (ptm160) cc_final: 0.5982 (ptm160) REVERT: A 144 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5798 (pp) REVERT: A 150 TYR cc_start: 0.7699 (t80) cc_final: 0.7459 (t80) REVERT: B 123 VAL cc_start: 0.8093 (p) cc_final: 0.7864 (m) REVERT: B 132 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5689 (ptm160) REVERT: D 90 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7263 (mtp-110) outliers start: 33 outliers final: 15 residues processed: 114 average time/residue: 0.3407 time to fit residues: 41.5939 Evaluate side-chains 120 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 90 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 2 optimal weight: 0.0770 chunk 63 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.232202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.205979 restraints weight = 7841.694| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 2.52 r_work: 0.4612 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6402 Z= 0.124 Angle : 0.643 9.710 8754 Z= 0.309 Chirality : 0.042 0.153 1026 Planarity : 0.006 0.048 1130 Dihedral : 5.827 46.888 897 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.31 % Allowed : 18.73 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.97 (0.30), residues: 802 helix: 1.94 (0.30), residues: 281 sheet: 0.08 (0.45), residues: 139 loop : -0.04 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 171 TYR 0.016 0.001 TYR A 150 PHE 0.027 0.002 PHE C 27 TRP 0.012 0.002 TRP A 106 HIS 0.001 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6402) covalent geometry : angle 0.64330 ( 8754) hydrogen bonds : bond 0.02913 ( 294) hydrogen bonds : angle 4.55211 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.4600 (tmt) REVERT: A 115 GLN cc_start: 0.6433 (mm-40) cc_final: 0.6006 (mm110) REVERT: A 132 ARG cc_start: 0.6180 (ptm160) cc_final: 0.5941 (ptm160) REVERT: A 136 LEU cc_start: 0.4458 (mt) cc_final: 0.4141 (mt) REVERT: A 144 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6205 (pp) REVERT: A 150 TYR cc_start: 0.7564 (t80) cc_final: 0.7345 (t80) REVERT: B 123 VAL cc_start: 0.8064 (p) cc_final: 0.7825 (m) REVERT: B 132 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.5710 (ptm160) REVERT: C 76 MET cc_start: 0.3566 (ttt) cc_final: 0.0648 (mmm) outliers start: 23 outliers final: 14 residues processed: 114 average time/residue: 0.3257 time to fit residues: 40.0761 Evaluate side-chains 121 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 2 optimal weight: 0.3980 chunk 56 optimal weight: 0.0570 chunk 10 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 0.0370 overall best weight: 0.1372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.234428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.208244 restraints weight = 7844.251| |-----------------------------------------------------------------------------| r_work (start): 0.4735 rms_B_bonded: 2.61 r_work: 0.4626 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6402 Z= 0.110 Angle : 0.628 9.377 8754 Z= 0.300 Chirality : 0.041 0.148 1026 Planarity : 0.006 0.047 1130 Dihedral : 5.599 44.168 897 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.59 % Allowed : 19.45 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.18 (0.30), residues: 802 helix: 2.04 (0.31), residues: 281 sheet: 0.23 (0.45), residues: 139 loop : 0.13 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.013 0.001 TYR C 58 PHE 0.025 0.001 PHE C 27 TRP 0.014 0.002 TRP A 106 HIS 0.002 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6402) covalent geometry : angle 0.62754 ( 8754) hydrogen bonds : bond 0.02803 ( 294) hydrogen bonds : angle 4.36959 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.4930 (OUTLIER) cc_final: 0.4482 (tmt) REVERT: A 115 GLN cc_start: 0.6432 (mm-40) cc_final: 0.5952 (mm110) REVERT: B 123 VAL cc_start: 0.8047 (p) cc_final: 0.7777 (m) REVERT: C 76 MET cc_start: 0.3397 (ttt) cc_final: 0.0789 (mtp) REVERT: D 76 MET cc_start: 0.3437 (ttt) cc_final: 0.0123 (mmt) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.3158 time to fit residues: 38.1689 Evaluate side-chains 114 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 39 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.230129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.204384 restraints weight = 7782.204| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 2.55 r_work: 0.4583 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6402 Z= 0.153 Angle : 0.674 10.495 8754 Z= 0.323 Chirality : 0.043 0.181 1026 Planarity : 0.006 0.051 1130 Dihedral : 5.745 45.564 897 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.88 % Allowed : 20.17 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.03 (0.30), residues: 802 helix: 1.92 (0.30), residues: 281 sheet: 0.22 (0.45), residues: 139 loop : 0.01 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.011 0.001 TYR C 58 PHE 0.026 0.002 PHE C 27 TRP 0.020 0.003 TRP B 106 HIS 0.002 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6402) covalent geometry : angle 0.67368 ( 8754) hydrogen bonds : bond 0.03166 ( 294) hydrogen bonds : angle 4.43713 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4529 (tmt) REVERT: A 115 GLN cc_start: 0.6479 (mm-40) cc_final: 0.5993 (mm110) REVERT: B 123 VAL cc_start: 0.8144 (p) cc_final: 0.7899 (m) REVERT: B 132 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5725 (ptm160) REVERT: B 144 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.5957 (pt) REVERT: C 76 MET cc_start: 0.3469 (ttt) cc_final: 0.0762 (mtp) REVERT: D 76 MET cc_start: 0.2999 (ttt) cc_final: -0.0142 (mmt) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 0.3071 time to fit residues: 36.0464 Evaluate side-chains 115 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 0.0370 chunk 60 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.230735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.205080 restraints weight = 7769.728| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 2.48 r_work: 0.4612 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6402 Z= 0.135 Angle : 0.651 9.807 8754 Z= 0.313 Chirality : 0.042 0.147 1026 Planarity : 0.006 0.048 1130 Dihedral : 5.727 48.482 897 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.59 % Allowed : 20.32 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.01 (0.30), residues: 802 helix: 1.81 (0.30), residues: 285 sheet: 0.20 (0.44), residues: 139 loop : 0.07 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.012 0.001 TYR C 58 PHE 0.024 0.001 PHE C 27 TRP 0.021 0.002 TRP D 106 HIS 0.002 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6402) covalent geometry : angle 0.65124 ( 8754) hydrogen bonds : bond 0.02954 ( 294) hydrogen bonds : angle 4.41968 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.52 seconds wall clock time: 38 minutes 18.77 seconds (2298.77 seconds total)