Starting phenix.real_space_refine on Tue Aug 4 23:37:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22gm_68264/08_2026/22gm_68264.cif Found real_map, /net/cci-nas-00/data/ceres_data/22gm_68264/08_2026/22gm_68264.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/22gm_68264/08_2026/22gm_68264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22gm_68264/08_2026/22gm_68264.map" model { file = "/net/cci-nas-00/data/ceres_data/22gm_68264/08_2026/22gm_68264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22gm_68264/08_2026/22gm_68264.cif" } 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= 0.003 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 C 4687 2.51 5 N 1227 2.21 5 O 1353 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7309 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2446 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2612 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 307} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.62, per 1000 atoms: 0.22 Number of scatterers: 7309 At special positions: 0 Unit cell: (79.98, 98.58, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 6 15.00 O 1353 8.00 N 1227 7.00 C 4687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 47 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 54 " distance=2.10 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 188 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.02 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.02 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: 0.65 Conformation dependent library (CDL) restraints added in 503.0 milliseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 34.3% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.512A pdb=" N TYR C 23 " --> pdb=" O LYS C 19 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 25 " --> pdb=" O CYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 44 through 62 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'R' and resid 34 through 66 removed outlier: 3.991A pdb=" N PHE R 64 " --> pdb=" O TRP R 60 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 88 Processing helix chain 'R' and resid 88 through 98 removed outlier: 3.501A pdb=" N LEU R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 139 Proline residue: R 113 - end of helix removed outlier: 3.574A pdb=" N LEU R 117 " --> pdb=" O PRO R 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 149 through 174 removed outlier: 4.026A pdb=" N ILE R 155 " --> pdb=" O GLY R 151 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 195 through 211 Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 237 through 265 Proline residue: R 257 - end of helix removed outlier: 3.687A pdb=" N ILE R 263 " --> pdb=" O GLN R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 289 removed outlier: 4.640A pdb=" N SER R 283 " --> pdb=" O LYS R 279 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU R 284 " --> pdb=" O LYS R 280 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER R 287 " --> pdb=" O SER R 283 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA R 289 " --> pdb=" O CYS R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 303 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 306 through 314 removed outlier: 3.669A pdb=" N ARG R 310 " --> pdb=" O GLY R 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.220A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 292 through 296 removed outlier: 4.101A pdb=" N HIS A 295 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing sheet with id=AA1, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA2, first strand: chain 'R' and resid 361 through 364 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.239A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.239A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.467A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.467A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.798A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.798A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 183 through 188 Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.134A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2070 1.33 - 1.48: 2292 1.48 - 1.63: 3063 1.63 - 1.78: 16 1.78 - 1.93: 30 Bond restraints: 7471 Sorted by residual: bond pdb=" OG1 TPO R 360 " pdb=" P TPO R 360 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO R 359 " pdb=" P TPO R 359 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O2P SEP R 363 " pdb=" P SEP R 363 " ideal model delta sigma weight residual 1.610 1.503 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" O1P SEP R 363 " pdb=" P SEP R 363 " ideal model delta sigma weight residual 1.610 1.505 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" O3P SEP R 363 " pdb=" P SEP R 363 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 7466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 9186 2.63 - 5.26: 866 5.26 - 7.88: 105 7.88 - 10.51: 10 10.51 - 13.14: 4 Bond angle restraints: 10171 Sorted by residual: angle pdb=" CA ILE R 169 " pdb=" C ILE R 169 " pdb=" N PRO R 170 " ideal model delta sigma weight residual 120.83 117.40 3.43 6.10e-01 2.69e+00 3.16e+01 angle pdb=" N ILE R 91 " pdb=" CA ILE R 91 " pdb=" C ILE R 91 " ideal model delta sigma weight residual 110.82 105.97 4.85 9.70e-01 1.06e+00 2.50e+01 angle pdb=" C VAL L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.78 124.89 -5.11 1.03e+00 9.43e-01 2.46e+01 angle pdb=" N GLY C 73 " pdb=" CA GLY C 73 " pdb=" C GLY C 73 " ideal model delta sigma weight residual 114.67 109.28 5.39 1.10e+00 8.26e-01 2.40e+01 angle pdb=" N PHE A 244 " pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 111.14 105.90 5.24 1.08e+00 8.57e-01 2.35e+01 ... (remaining 10166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4269 17.05 - 34.10: 167 34.10 - 51.14: 26 51.14 - 68.19: 7 68.19 - 85.24: 7 Dihedral angle restraints: 4476 sinusoidal: 1724 harmonic: 2752 Sorted by residual: dihedral pdb=" CA SER L 8 " pdb=" C SER L 8 " pdb=" N PRO L 9 " pdb=" CA PRO L 9 " ideal model delta harmonic sigma weight residual 0.00 25.88 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PHE R 182 " pdb=" C PHE R 182 " pdb=" N PRO R 183 " pdb=" CA PRO R 183 " ideal model delta harmonic sigma weight residual 0.00 -25.78 25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 54 " pdb=" CB CYS C 54 " ideal model delta sinusoidal sigma weight residual 93.00 57.07 35.93 1 1.00e+01 1.00e-02 1.83e+01 ... (remaining 4473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 795 0.076 - 0.153: 290 0.153 - 0.229: 76 0.229 - 0.305: 11 0.305 - 0.382: 8 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CG LEU R 89 " pdb=" CB LEU R 89 " pdb=" CD1 LEU R 89 " pdb=" CD2 LEU R 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA PHE H 105 " pdb=" N PHE H 105 " pdb=" C PHE H 105 " pdb=" CB PHE H 105 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB VAL H 5 " pdb=" CA VAL H 5 " pdb=" CG1 VAL H 5 " pdb=" CG2 VAL H 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 1177 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 236 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ARG R 236 " -0.076 2.00e-02 2.50e+03 pdb=" O ARG R 236 " 0.029 2.00e-02 2.50e+03 pdb=" N SER R 237 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.056 2.00e-02 2.50e+03 2.87e-02 1.65e+01 pdb=" CG TYR L 92 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 192 " 0.050 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYR R 192 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 192 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR R 192 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR R 192 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR R 192 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR R 192 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 192 " 0.032 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2493 2.83 - 3.35: 6909 3.35 - 3.87: 12401 3.87 - 4.38: 14548 4.38 - 4.90: 24200 Nonbonded interactions: 60551 Sorted by model distance: nonbonded pdb=" N VAL A 53 " pdb=" O PHE A 87 " model vdw 2.318 3.120 nonbonded pdb=" N ASP H 65 " pdb=" OD1 ASP H 65 " model vdw 2.352 3.120 nonbonded pdb=" NH1 ARG C 40 " pdb=" OD2 ASP R 27 " model vdw 2.363 3.120 nonbonded pdb=" NE ARG A 62 " pdb=" O ALA A 139 " model vdw 2.376 3.120 nonbonded pdb=" NZ LYS A 95 " pdb=" OE2 GLU A 118 " model vdw 2.385 3.120 ... (remaining 60546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.310 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.018 0.121 7477 Z= 0.968 Angle : 1.615 13.140 10183 Z= 1.046 Chirality : 0.086 0.382 1180 Planarity : 0.008 0.045 1272 Dihedral : 10.174 85.240 2678 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.17 (0.27), residues: 914 helix: -1.42 (0.27), residues: 282 sheet: 0.93 (0.32), residues: 260 loop : -1.43 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 175 TYR 0.056 0.007 TYR L 92 PHE 0.038 0.004 PHE H 105 TRP 0.030 0.005 TRP L 36 HIS 0.009 0.002 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.01774 / 0.97 ( 7471) covalent geometry : angle 1.61245 / 1.05 (10171) SS BOND : bond 0.03087 / 1.51 ( 6) SS BOND : angle 3.25058 / 2.15 ( 12) hydrogen bonds : bond 0.17938 / 12.15 ( 381) hydrogen bonds : angle 8.70999 / 6.40 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 239 LYS cc_start: 0.7883 (pttm) cc_final: 0.7562 (mmtm) REVERT: R 312 ARG cc_start: 0.4191 (tmt-80) cc_final: 0.3140 (tpt170) REVERT: A 63 TYR cc_start: 0.7359 (t80) cc_final: 0.6930 (t80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.4174 time to fit residues: 83.8881 Evaluate side-chains 111 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 29 ASN ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN A 101 GLN A 219 HIS A 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.086005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.074962 restraints weight = 24703.739| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.80 r_work: 0.3624 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7477 Z= 0.211 Angle : 0.743 12.103 10183 Z= 0.392 Chirality : 0.047 0.181 1180 Planarity : 0.005 0.038 1272 Dihedral : 6.225 73.156 1032 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.43 % Allowed : 12.94 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.09 (0.28), residues: 914 helix: 0.22 (0.30), residues: 280 sheet: 1.11 (0.33), residues: 248 loop : -1.01 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 285 TYR 0.017 0.002 TYR A 63 PHE 0.020 0.002 PHE H 105 TRP 0.024 0.002 TRP H 106 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 ( 7471) covalent geometry : angle 0.74179 / 0.39 (10171) SS BOND : bond 0.01293 / 0.67 ( 6) SS BOND : angle 1.64056 / 1.04 ( 12) hydrogen bonds : bond 0.05616 / 3.88 ( 381) hydrogen bonds : angle 6.23826 / 4.57 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: C 18 VAL cc_start: 0.6485 (t) cc_final: 0.6100 (t) REVERT: C 36 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.6085 (pm20) REVERT: C 48 ILE cc_start: 0.8475 (pt) cc_final: 0.8181 (pp) REVERT: R 258 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7866 (t80) REVERT: R 312 ARG cc_start: 0.3694 (tmt-80) cc_final: 0.2250 (tpt170) REVERT: H 93 ASP cc_start: 0.8191 (m-30) cc_final: 0.7922 (m-30) outliers start: 27 outliers final: 13 residues processed: 151 average time/residue: 0.3926 time to fit residues: 63.0832 Evaluate side-chains 119 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 258 TYR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 286 VAL Chi-restraints excluded: chain R residue 305 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 250 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.0000 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 73 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.094879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.083768 restraints weight = 24215.970| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.83 r_work: 0.3631 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7477 Z= 0.154 Angle : 0.663 10.303 10183 Z= 0.343 Chirality : 0.044 0.140 1180 Planarity : 0.005 0.036 1272 Dihedral : 6.061 73.016 1032 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 3.17 % Allowed : 15.48 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.33 (0.28), residues: 914 helix: 0.60 (0.30), residues: 282 sheet: 1.28 (0.32), residues: 253 loop : -0.78 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 285 TYR 0.017 0.002 TYR A 63 PHE 0.018 0.002 PHE C 51 TRP 0.018 0.002 TRP H 106 HIS 0.006 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7471) covalent geometry : angle 0.66086 / 0.34 (10171) SS BOND : bond 0.00567 / 0.28 ( 6) SS BOND : angle 1.71827 / 1.01 ( 12) hydrogen bonds : bond 0.04780 / 3.30 ( 381) hydrogen bonds : angle 5.66959 / 4.19 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.300 Fit side-chains REVERT: C 3 GLN cc_start: 0.5804 (mp10) cc_final: 0.5414 (mp10) REVERT: C 65 ILE cc_start: 0.8694 (tp) cc_final: 0.8435 (tp) REVERT: R 258 TYR cc_start: 0.8083 (t80) cc_final: 0.7672 (t80) REVERT: R 312 ARG cc_start: 0.3498 (OUTLIER) cc_final: 0.2109 (tpt170) REVERT: H 93 ASP cc_start: 0.8171 (m-30) cc_final: 0.7891 (m-30) REVERT: A 293 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5355 (pp) outliers start: 25 outliers final: 10 residues processed: 136 average time/residue: 0.4540 time to fit residues: 65.7261 Evaluate side-chains 110 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 237 SER Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 293 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 82 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.0070 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN A 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.084782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.074087 restraints weight = 25284.961| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.76 r_work: 0.3581 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7477 Z= 0.181 Angle : 0.704 15.023 10183 Z= 0.360 Chirality : 0.044 0.246 1180 Planarity : 0.005 0.043 1272 Dihedral : 6.039 72.178 1032 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 3.05 % Allowed : 17.39 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.43 (0.28), residues: 914 helix: 0.74 (0.30), residues: 282 sheet: 1.33 (0.32), residues: 252 loop : -0.76 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 285 TYR 0.019 0.002 TYR A 21 PHE 0.015 0.001 PHE H 105 TRP 0.013 0.001 TRP H 106 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 7471) covalent geometry : angle 0.67801 / 0.35 (10171) SS BOND : bond 0.00731 / 0.36 ( 6) SS BOND : angle 5.52327 / 3.06 ( 12) hydrogen bonds : bond 0.04595 / 3.18 ( 381) hydrogen bonds : angle 5.52475 / 4.14 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.311 Fit side-chains REVERT: C 3 GLN cc_start: 0.5978 (mp10) cc_final: 0.5639 (mp10) REVERT: C 18 VAL cc_start: 0.7005 (t) cc_final: 0.6780 (t) REVERT: C 65 ILE cc_start: 0.8641 (tp) cc_final: 0.8399 (pp) REVERT: R 258 TYR cc_start: 0.8124 (t80) cc_final: 0.7793 (t80) REVERT: R 312 ARG cc_start: 0.3665 (OUTLIER) cc_final: 0.2237 (tpt170) REVERT: H 93 ASP cc_start: 0.8123 (m-30) cc_final: 0.7795 (m-30) REVERT: H 111 ASP cc_start: 0.7420 (m-30) cc_final: 0.7175 (m-30) outliers start: 24 outliers final: 12 residues processed: 121 average time/residue: 0.4329 time to fit residues: 56.3999 Evaluate side-chains 113 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.084823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.074161 restraints weight = 25159.071| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.73 r_work: 0.3607 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7477 Z= 0.160 Angle : 0.659 10.808 10183 Z= 0.337 Chirality : 0.043 0.181 1180 Planarity : 0.005 0.037 1272 Dihedral : 5.901 70.483 1032 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 3.05 % Allowed : 17.26 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.56 (0.28), residues: 914 helix: 0.90 (0.30), residues: 284 sheet: 1.35 (0.32), residues: 253 loop : -0.70 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 178 TYR 0.018 0.001 TYR A 21 PHE 0.023 0.001 PHE R 252 TRP 0.011 0.001 TRP H 106 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 7471) covalent geometry : angle 0.64147 / 0.33 (10171) SS BOND : bond 0.01265 / 0.60 ( 6) SS BOND : angle 4.47416 / 2.50 ( 12) hydrogen bonds : bond 0.04311 / 3.00 ( 381) hydrogen bonds : angle 5.31922 / 3.99 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.238 Fit side-chains REVERT: C 3 GLN cc_start: 0.5932 (mp10) cc_final: 0.5687 (mp10) REVERT: C 36 GLN cc_start: 0.6607 (pm20) cc_final: 0.6349 (pm20) REVERT: C 61 LEU cc_start: 0.7915 (tm) cc_final: 0.7662 (tt) REVERT: C 65 ILE cc_start: 0.8478 (tp) cc_final: 0.8214 (pp) REVERT: R 239 LYS cc_start: 0.7785 (pttm) cc_final: 0.7162 (mmtm) REVERT: R 258 TYR cc_start: 0.8111 (t80) cc_final: 0.7849 (t80) REVERT: R 312 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.2068 (tpt170) REVERT: H 49 GLU cc_start: 0.7807 (tt0) cc_final: 0.7601 (tp30) REVERT: H 111 ASP cc_start: 0.7413 (m-30) cc_final: 0.7109 (m-30) outliers start: 24 outliers final: 13 residues processed: 127 average time/residue: 0.4550 time to fit residues: 61.7125 Evaluate side-chains 117 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 155 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 0.0370 chunk 52 optimal weight: 0.4980 chunk 67 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.085106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.074542 restraints weight = 25257.085| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.75 r_work: 0.3619 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7477 Z= 0.137 Angle : 0.647 10.513 10183 Z= 0.331 Chirality : 0.043 0.211 1180 Planarity : 0.005 0.045 1272 Dihedral : 5.718 68.734 1032 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 3.43 % Allowed : 17.39 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.76 (0.29), residues: 914 helix: 1.14 (0.31), residues: 283 sheet: 1.52 (0.33), residues: 245 loop : -0.64 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 178 TYR 0.018 0.001 TYR A 21 PHE 0.021 0.001 PHE R 252 TRP 0.011 0.001 TRP H 106 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 7471) covalent geometry : angle 0.63546 / 0.33 (10171) SS BOND : bond 0.00622 / 0.31 ( 6) SS BOND : angle 3.61488 / 1.98 ( 12) hydrogen bonds : bond 0.04045 / 2.82 ( 381) hydrogen bonds : angle 5.16701 / 3.88 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: C 3 GLN cc_start: 0.5746 (mp10) cc_final: 0.5523 (mp10) REVERT: R 239 LYS cc_start: 0.7753 (pttm) cc_final: 0.7124 (mmtm) REVERT: R 258 TYR cc_start: 0.8092 (t80) cc_final: 0.7876 (t80) REVERT: R 312 ARG cc_start: 0.3440 (OUTLIER) cc_final: 0.2817 (ptm-80) REVERT: H 111 ASP cc_start: 0.7489 (m-30) cc_final: 0.7145 (m-30) REVERT: L 6 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8904 (p) REVERT: L 83 ASP cc_start: 0.8377 (m-30) cc_final: 0.8138 (m-30) outliers start: 27 outliers final: 11 residues processed: 126 average time/residue: 0.4586 time to fit residues: 61.6938 Evaluate side-chains 116 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.084595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.073929 restraints weight = 25265.228| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.74 r_work: 0.3607 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7477 Z= 0.155 Angle : 0.643 9.834 10183 Z= 0.330 Chirality : 0.043 0.184 1180 Planarity : 0.005 0.083 1272 Dihedral : 5.630 67.397 1032 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 2.92 % Allowed : 18.27 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.90 (0.29), residues: 914 helix: 1.21 (0.31), residues: 285 sheet: 1.63 (0.33), residues: 239 loop : -0.51 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 65 TYR 0.020 0.002 TYR A 21 PHE 0.019 0.001 PHE R 252 TRP 0.010 0.001 TRP H 106 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 7471) covalent geometry : angle 0.63763 / 0.33 (10171) SS BOND : bond 0.01040 / 0.51 ( 6) SS BOND : angle 2.46376 / 1.45 ( 12) hydrogen bonds : bond 0.04057 / 2.83 ( 381) hydrogen bonds : angle 5.14961 / 3.84 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 239 LYS cc_start: 0.7786 (pttm) cc_final: 0.7198 (mmtm) REVERT: R 258 TYR cc_start: 0.8120 (t80) cc_final: 0.7911 (t80) REVERT: R 312 ARG cc_start: 0.3647 (OUTLIER) cc_final: 0.2048 (tpt170) REVERT: H 111 ASP cc_start: 0.7396 (m-30) cc_final: 0.7069 (m-30) REVERT: L 6 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8912 (p) REVERT: L 83 ASP cc_start: 0.8366 (m-30) cc_final: 0.8158 (m-30) outliers start: 23 outliers final: 14 residues processed: 125 average time/residue: 0.4691 time to fit residues: 62.5591 Evaluate side-chains 120 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.083445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.072507 restraints weight = 25417.973| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.79 r_work: 0.3570 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7477 Z= 0.202 Angle : 0.692 10.912 10183 Z= 0.353 Chirality : 0.044 0.161 1180 Planarity : 0.005 0.038 1272 Dihedral : 5.719 65.826 1032 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.30 % Allowed : 18.65 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.75 (0.28), residues: 914 helix: 1.13 (0.31), residues: 284 sheet: 1.38 (0.32), residues: 263 loop : -0.64 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 65 TYR 0.028 0.002 TYR R 174 PHE 0.020 0.002 PHE H 105 TRP 0.011 0.002 TRP H 106 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 7471) covalent geometry : angle 0.68786 / 0.35 (10171) SS BOND : bond 0.01012 / 0.49 ( 6) SS BOND : angle 2.37190 / 1.41 ( 12) hydrogen bonds : bond 0.04350 / 3.01 ( 381) hydrogen bonds : angle 5.27312 / 3.94 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 GLU cc_start: 0.7462 (tp30) cc_final: 0.7262 (tp30) REVERT: R 258 TYR cc_start: 0.8228 (t80) cc_final: 0.8017 (t80) REVERT: R 312 ARG cc_start: 0.4158 (OUTLIER) cc_final: 0.2283 (tpt170) REVERT: H 111 ASP cc_start: 0.7413 (m-30) cc_final: 0.7118 (m-30) REVERT: A 192 MET cc_start: 0.5521 (OUTLIER) cc_final: 0.5116 (ptp) outliers start: 26 outliers final: 12 residues processed: 117 average time/residue: 0.4220 time to fit residues: 52.7088 Evaluate side-chains 111 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 232 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.083529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.073035 restraints weight = 24839.510| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.72 r_work: 0.3590 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7477 Z= 0.168 Angle : 0.664 9.045 10183 Z= 0.344 Chirality : 0.043 0.155 1180 Planarity : 0.004 0.037 1272 Dihedral : 5.673 64.601 1032 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.41 % Allowed : 19.54 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.81 (0.29), residues: 914 helix: 1.22 (0.31), residues: 284 sheet: 1.44 (0.32), residues: 257 loop : -0.64 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 65 TYR 0.020 0.001 TYR A 21 PHE 0.015 0.002 PHE R 252 TRP 0.008 0.001 TRP H 106 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 7471) covalent geometry : angle 0.65940 / 0.34 (10171) SS BOND : bond 0.00878 / 0.43 ( 6) SS BOND : angle 2.46699 / 1.51 ( 12) hydrogen bonds : bond 0.04208 / 2.90 ( 381) hydrogen bonds : angle 5.23070 / 3.89 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 7 GLU cc_start: 0.7521 (tp30) cc_final: 0.7317 (tp30) REVERT: R 86 CYS cc_start: 0.7593 (p) cc_final: 0.7292 (m) REVERT: R 239 LYS cc_start: 0.7939 (pttm) cc_final: 0.7463 (mmtm) REVERT: R 258 TYR cc_start: 0.8145 (t80) cc_final: 0.7943 (t80) REVERT: R 312 ARG cc_start: 0.4158 (OUTLIER) cc_final: 0.2181 (tpt170) REVERT: H 111 ASP cc_start: 0.7395 (m-30) cc_final: 0.7092 (m-30) REVERT: A 49 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5052 (tppt) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.4160 time to fit residues: 50.5076 Evaluate side-chains 115 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 232 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.083054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.072508 restraints weight = 24785.822| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.73 r_work: 0.3580 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7477 Z= 0.191 Angle : 0.692 10.758 10183 Z= 0.354 Chirality : 0.044 0.155 1180 Planarity : 0.005 0.039 1272 Dihedral : 5.672 63.915 1032 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.16 % Allowed : 20.43 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.79 (0.28), residues: 914 helix: 1.21 (0.31), residues: 284 sheet: 1.44 (0.32), residues: 257 loop : -0.67 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 103 TYR 0.021 0.002 TYR A 21 PHE 0.021 0.002 PHE R 252 TRP 0.010 0.002 TRP H 50 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 7471) covalent geometry : angle 0.68615 / 0.35 (10171) SS BOND : bond 0.00845 / 0.41 ( 6) SS BOND : angle 2.62233 / 1.54 ( 12) hydrogen bonds : bond 0.04317 / 2.98 ( 381) hydrogen bonds : angle 5.24575 / 3.91 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 86 CYS cc_start: 0.7651 (p) cc_final: 0.7333 (m) REVERT: R 239 LYS cc_start: 0.8030 (pttm) cc_final: 0.7538 (mmtm) REVERT: R 258 TYR cc_start: 0.8155 (t80) cc_final: 0.7950 (t80) REVERT: R 312 ARG cc_start: 0.4270 (OUTLIER) cc_final: 0.2221 (tpt170) REVERT: H 111 ASP cc_start: 0.7411 (m-30) cc_final: 0.7101 (m-30) REVERT: A 49 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.5093 (tppt) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 0.4511 time to fit residues: 51.4572 Evaluate side-chains 110 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 248 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.0060 chunk 70 optimal weight: 0.0030 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.084672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.074396 restraints weight = 24711.873| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.67 r_work: 0.3624 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7477 Z= 0.131 Angle : 0.666 9.412 10183 Z= 0.342 Chirality : 0.043 0.147 1180 Planarity : 0.004 0.037 1272 Dihedral : 5.555 63.269 1032 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.78 % Allowed : 20.81 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 914 helix: 1.31 (0.31), residues: 284 sheet: 1.68 (0.33), residues: 239 loop : -0.61 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 103 TYR 0.018 0.001 TYR A 21 PHE 0.022 0.001 PHE R 252 TRP 0.015 0.001 TRP H 106 HIS 0.002 0.000 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7471) covalent geometry : angle 0.65911 / 0.34 (10171) SS BOND : bond 0.00751 / 0.36 ( 6) SS BOND : angle 2.78410 / 1.59 ( 12) hydrogen bonds : bond 0.03920 / 2.71 ( 381) hydrogen bonds : angle 5.05697 / 3.75 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.91 seconds wall clock time: 42 minutes 46.29 seconds (2566.29 seconds total)