Starting phenix.real_space_refine on Thu Sep 18 08:31:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vww_43604/09_2025/8vww_43604.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vww_43604/09_2025/8vww_43604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vww_43604/09_2025/8vww_43604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vww_43604/09_2025/8vww_43604.map" model { file = "/net/cci-nas-00/data/ceres_data/8vww_43604/09_2025/8vww_43604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vww_43604/09_2025/8vww_43604.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1936 atoms to isotropic. 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 S 28 5.16 5 C 4411 2.51 5 N 1158 2.21 5 O 1349 1.98 5 H 6855 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13801 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 4013 Classifications: {'peptide': 247} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "B" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1866 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "C" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1595 Classifications: {'peptide': 107} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3199 Classifications: {'peptide': 217} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3128 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 194} Chain breaks: 1 Time building chain proxies: 2.60, per 1000 atoms: 0.19 Number of scatterers: 13801 At special positions: 0 Unit cell: (73.3216, 94.1516, 153.309, 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 28 16.00 O 1349 8.00 N 1158 7.00 C 4411 6.00 H 6855 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 295 " distance=2.02 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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: 1.14 Conformation dependent library (CDL) restraints added in 431.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 19 sheets defined 10.6% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 394 through 398 removed outlier: 4.103A pdb=" N ILE A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.505A pdb=" N ASN B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.794A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 185 through 189 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.596A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 355 removed outlier: 6.941A pdb=" N SER A 360 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER A 442 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 436 " --> pdb=" O CYS A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.583A pdb=" N ILE A 375 " --> pdb=" O ILE A 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.199A pdb=" N VAL A 385 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LYS A 503 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.595A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 18 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.937A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.642A pdb=" N ALA B 100E" --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.302A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 50 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.302A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN C 90 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.650A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.156A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER H 177 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA H 168 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER H 179 " --> pdb=" O PHE H 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.396A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.892A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.563A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU L 33 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA L 50 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.557A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 145 through 149 removed outlier: 3.702A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 660 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: 3.28 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6855 1.03 - 1.23: 6 1.23 - 1.42: 3002 1.42 - 1.62: 4058 1.62 - 1.81: 34 Bond restraints: 13955 Sorted by residual: bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.64e-01 bond pdb=" CB CYS A 287 " pdb=" SG CYS A 287 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.61e-01 bond pdb=" CB CYS B 92 " pdb=" SG CYS B 92 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.34e-01 bond pdb=" CB GLN A 373 " pdb=" CG GLN A 373 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.88e-01 bond pdb=" ND2 ASN A 402 " pdb="HD22 ASN A 402 " ideal model delta sigma weight residual 0.860 0.846 0.014 2.00e-02 2.50e+03 4.88e-01 ... (remaining 13950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 24534 1.49 - 2.98: 573 2.98 - 4.47: 59 4.47 - 5.96: 5 5.96 - 7.45: 2 Bond angle restraints: 25173 Sorted by residual: angle pdb=" N PRO H 149 " pdb=" CA PRO H 149 " pdb=" C PRO H 149 " ideal model delta sigma weight residual 110.21 113.99 -3.78 1.64e+00 3.72e-01 5.31e+00 angle pdb=" N TYR A 359 " pdb=" CA TYR A 359 " pdb=" C TYR A 359 " ideal model delta sigma weight residual 108.79 105.26 3.53 1.53e+00 4.27e-01 5.31e+00 angle pdb=" N HIS A 431 " pdb=" CA HIS A 431 " pdb=" C HIS A 431 " ideal model delta sigma weight residual 108.02 104.04 3.98 1.78e+00 3.16e-01 4.99e+00 angle pdb=" N LYS H 201 " pdb=" CA LYS H 201 " pdb=" C LYS H 201 " ideal model delta sigma weight residual 109.81 114.67 -4.86 2.21e+00 2.05e-01 4.84e+00 angle pdb=" N ILE A 309 " pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 109.34 113.84 -4.50 2.08e+00 2.31e-01 4.68e+00 ... (remaining 25168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5997 17.82 - 35.63: 425 35.63 - 53.45: 141 53.45 - 71.27: 98 71.27 - 89.08: 7 Dihedral angle restraints: 6668 sinusoidal: 3593 harmonic: 3075 Sorted by residual: dihedral pdb=" CA ALA B 88 " pdb=" C ALA B 88 " pdb=" N VAL B 89 " pdb=" CA VAL B 89 " ideal model delta harmonic sigma weight residual 180.00 153.45 26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO H 98 " pdb=" C PRO H 98 " pdb=" N ASP H 99 " pdb=" CA ASP H 99 " ideal model delta harmonic sigma weight residual 180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE H 69 " pdb=" C ILE H 69 " pdb=" N SER H 70 " pdb=" CA SER H 70 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 674 0.032 - 0.065: 260 0.065 - 0.097: 91 0.097 - 0.130: 57 0.130 - 0.162: 9 Chirality restraints: 1091 Sorted by residual: chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA VAL A 433 " pdb=" N VAL A 433 " pdb=" C VAL A 433 " pdb=" CB VAL A 433 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1088 not shown) Planarity restraints: 2068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 496 " 0.029 2.00e-02 2.50e+03 4.99e-02 3.74e+01 pdb=" CD GLN A 496 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLN A 496 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN A 496 " 0.086 2.00e-02 2.50e+03 pdb="HE21 GLN A 496 " 0.005 2.00e-02 2.50e+03 pdb="HE22 GLN A 496 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 402 " -0.040 2.00e-02 2.50e+03 4.83e-02 3.49e+01 pdb=" CG ASN A 402 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 402 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 402 " 0.075 2.00e-02 2.50e+03 pdb="HD21 ASN A 402 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASN A 402 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 248 " 0.024 2.00e-02 2.50e+03 2.95e-02 1.31e+01 pdb=" CG ASN A 248 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 248 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 248 " -0.047 2.00e-02 2.50e+03 pdb="HD21 ASN A 248 " -0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 248 " 0.045 2.00e-02 2.50e+03 ... (remaining 2065 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 509 2.15 - 2.76: 26284 2.76 - 3.37: 37766 3.37 - 3.99: 49393 3.99 - 4.60: 76250 Nonbonded interactions: 190202 Sorted by model distance: nonbonded pdb=" HG1 THR A 367 " pdb=" OG SER A 370 " model vdw 1.533 2.450 nonbonded pdb=" O GLY A 350 " pdb=" H SER A 365 " model vdw 1.562 2.450 nonbonded pdb=" OE1 GLN L 6 " pdb=" H GLY L 101 " model vdw 1.587 2.450 nonbonded pdb=" O GLN L 124 " pdb=" HG SER L 127 " model vdw 1.595 2.450 nonbonded pdb=" H GLN L 79 " pdb=" OD2 ASP L 82 " model vdw 1.600 2.450 ... (remaining 190197 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 group one per residue 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: 6.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.080 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 0.031 7111 Z= 0.150 Angle : 0.637 7.449 9659 Z= 0.343 Chirality : 0.045 0.162 1091 Planarity : 0.006 0.063 1219 Dihedral : 13.699 89.083 2558 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.36 % Rotamer: Outliers : 2.05 % Allowed : 7.67 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.82 (0.27), residues: 883 helix: -1.07 (0.56), residues: 57 sheet: -0.13 (0.28), residues: 340 loop : -0.72 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG L 142 TYR 0.035 0.005 TYR C 87 PHE 0.015 0.002 PHE A 408 TRP 0.024 0.005 TRP B 100A HIS 0.009 0.003 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7100) covalent geometry : angle 0.63428 ( 9637) SS BOND : bond 0.00382 ( 11) SS BOND : angle 1.32899 ( 22) hydrogen bonds : bond 0.25068 ( 254) hydrogen bonds : angle 9.84470 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.8376 (t60) cc_final: 0.7901 (t60) REVERT: A 480 THR cc_start: 0.8008 (m) cc_final: 0.7796 (p) REVERT: B 13 GLN cc_start: 0.8050 (mp10) cc_final: 0.7681 (mp10) REVERT: B 33 TYR cc_start: 0.8155 (m-10) cc_final: 0.7904 (m-10) REVERT: B 75 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8567 (mmtt) REVERT: B 101 ASP cc_start: 0.7671 (p0) cc_final: 0.7431 (p0) REVERT: C 106 ILE cc_start: 0.6146 (mm) cc_final: 0.5819 (mm) REVERT: H 194 TYR cc_start: 0.8112 (m-80) cc_final: 0.7899 (m-80) REVERT: H 199 ASN cc_start: 0.8846 (t0) cc_final: 0.8638 (t0) REVERT: L 70 ASP cc_start: 0.8145 (t70) cc_final: 0.7817 (t0) REVERT: L 92 TYR cc_start: 0.8689 (t80) cc_final: 0.8376 (t80) REVERT: L 145 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7941 (mtmm) REVERT: L 167 ASP cc_start: 0.8535 (t70) cc_final: 0.7189 (m-30) outliers start: 16 outliers final: 3 residues processed: 233 average time/residue: 0.2490 time to fit residues: 73.1550 Evaluate side-chains 151 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 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 290 ASN A 301 GLN A 422 GLN H 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122337 restraints weight = 28081.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127017 restraints weight = 15229.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130064 restraints weight = 9924.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132003 restraints weight = 7290.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133415 restraints weight = 5867.379| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7111 Z= 0.178 Angle : 0.669 8.152 9659 Z= 0.356 Chirality : 0.045 0.167 1091 Planarity : 0.004 0.036 1219 Dihedral : 6.290 50.500 979 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.05 % Allowed : 12.79 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.36 (0.28), residues: 883 helix: 0.75 (0.69), residues: 53 sheet: -0.05 (0.28), residues: 348 loop : -0.41 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 289 TYR 0.016 0.002 TYR C 49 PHE 0.016 0.002 PHE A 321 TRP 0.012 0.001 TRP H 154 HIS 0.006 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7100) covalent geometry : angle 0.66775 ( 9637) SS BOND : bond 0.00419 ( 11) SS BOND : angle 1.05803 ( 22) hydrogen bonds : bond 0.05038 ( 254) hydrogen bonds : angle 7.37163 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6465 (pmm) REVERT: A 286 TRP cc_start: 0.8428 (t60) cc_final: 0.8063 (t60) REVERT: B 13 GLN cc_start: 0.8219 (mp10) cc_final: 0.7838 (mp10) REVERT: B 31 SER cc_start: 0.8115 (p) cc_final: 0.7881 (t) REVERT: C 18 ARG cc_start: 0.5775 (OUTLIER) cc_final: 0.5454 (ttt-90) REVERT: H 6 GLU cc_start: 0.8526 (mp0) cc_final: 0.8195 (mp0) REVERT: H 199 ASN cc_start: 0.8885 (t0) cc_final: 0.8660 (t0) REVERT: L 92 TYR cc_start: 0.8606 (t80) cc_final: 0.8342 (t80) REVERT: L 167 ASP cc_start: 0.7659 (t70) cc_final: 0.6847 (m-30) REVERT: L 169 LYS cc_start: 0.8114 (tppt) cc_final: 0.7544 (tppt) outliers start: 16 outliers final: 6 residues processed: 164 average time/residue: 0.2070 time to fit residues: 44.0395 Evaluate side-chains 142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 476 ASN ** H 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125639 restraints weight = 27467.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129837 restraints weight = 15493.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132658 restraints weight = 10361.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134361 restraints weight = 7724.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135664 restraints weight = 6290.180| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7111 Z= 0.174 Angle : 0.622 8.001 9659 Z= 0.323 Chirality : 0.043 0.156 1091 Planarity : 0.004 0.044 1219 Dihedral : 5.673 47.930 974 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.66 % Allowed : 14.58 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.28 (0.29), residues: 883 helix: 0.91 (0.70), residues: 55 sheet: -0.02 (0.27), residues: 353 loop : -0.35 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.013 0.002 TYR C 93 PHE 0.021 0.002 PHE L 209 TRP 0.011 0.002 TRP B 100A HIS 0.004 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 7100) covalent geometry : angle 0.62095 ( 9637) SS BOND : bond 0.00346 ( 11) SS BOND : angle 0.92103 ( 22) hydrogen bonds : bond 0.04354 ( 254) hydrogen bonds : angle 6.83679 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6673 (pmm) REVERT: A 286 TRP cc_start: 0.8357 (t60) cc_final: 0.8029 (t60) REVERT: H 6 GLU cc_start: 0.8451 (mp0) cc_final: 0.8214 (mp0) REVERT: L 167 ASP cc_start: 0.7463 (t70) cc_final: 0.6534 (m-30) outliers start: 13 outliers final: 8 residues processed: 147 average time/residue: 0.1812 time to fit residues: 36.4122 Evaluate side-chains 142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124766 restraints weight = 27270.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129385 restraints weight = 14590.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132290 restraints weight = 9439.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134283 restraints weight = 6943.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135506 restraints weight = 5536.690| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7111 Z= 0.148 Angle : 0.588 7.955 9659 Z= 0.306 Chirality : 0.043 0.154 1091 Planarity : 0.004 0.049 1219 Dihedral : 5.163 20.907 970 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.66 % Allowed : 15.60 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.13 (0.29), residues: 883 helix: 1.32 (0.72), residues: 54 sheet: 0.06 (0.28), residues: 348 loop : -0.27 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 18 TYR 0.012 0.002 TYR A 465 PHE 0.015 0.002 PHE L 209 TRP 0.010 0.001 TRP B 100A HIS 0.004 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7100) covalent geometry : angle 0.58738 ( 9637) SS BOND : bond 0.00309 ( 11) SS BOND : angle 0.92903 ( 22) hydrogen bonds : bond 0.03778 ( 254) hydrogen bonds : angle 6.48088 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6655 (pmm) REVERT: A 286 TRP cc_start: 0.8396 (t60) cc_final: 0.8004 (t60) REVERT: C 39 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6682 (mtpt) REVERT: H 6 GLU cc_start: 0.8457 (mp0) cc_final: 0.8094 (mp0) REVERT: L 167 ASP cc_start: 0.7477 (t70) cc_final: 0.6389 (m-30) REVERT: L 170 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6822 (m-30) outliers start: 13 outliers final: 6 residues processed: 143 average time/residue: 0.1770 time to fit residues: 34.3079 Evaluate side-chains 135 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN H 164 HIS L 55 GLN L 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114889 restraints weight = 29958.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119410 restraints weight = 16258.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122372 restraints weight = 10670.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124367 restraints weight = 7940.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125746 restraints weight = 6395.982| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7111 Z= 0.172 Angle : 0.594 8.795 9659 Z= 0.309 Chirality : 0.043 0.149 1091 Planarity : 0.003 0.031 1219 Dihedral : 5.063 20.608 970 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.53 % Allowed : 17.26 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.15 (0.29), residues: 883 helix: 1.10 (0.70), residues: 55 sheet: -0.02 (0.28), residues: 334 loop : -0.20 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 38 TYR 0.014 0.002 TYR L 49 PHE 0.013 0.002 PHE L 209 TRP 0.009 0.001 TRP B 100A HIS 0.004 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7100) covalent geometry : angle 0.59250 ( 9637) SS BOND : bond 0.00352 ( 11) SS BOND : angle 0.95566 ( 22) hydrogen bonds : bond 0.03693 ( 254) hydrogen bonds : angle 6.29334 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6813 (pmm) REVERT: A 286 TRP cc_start: 0.8472 (t60) cc_final: 0.8038 (t60) REVERT: B 13 GLN cc_start: 0.8011 (mp10) cc_final: 0.7743 (mp10) REVERT: C 39 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6952 (mtpt) REVERT: H 6 GLU cc_start: 0.8525 (mp0) cc_final: 0.8181 (mp0) REVERT: L 167 ASP cc_start: 0.7580 (t70) cc_final: 0.6259 (m-30) REVERT: L 170 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7166 (m-30) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.1867 time to fit residues: 33.6424 Evaluate side-chains 128 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 0.0970 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN B 105 GLN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117094 restraints weight = 29151.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121601 restraints weight = 15668.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124581 restraints weight = 10237.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126588 restraints weight = 7585.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127842 restraints weight = 6081.606| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7111 Z= 0.114 Angle : 0.552 7.744 9659 Z= 0.283 Chirality : 0.042 0.150 1091 Planarity : 0.003 0.030 1219 Dihedral : 4.801 19.600 970 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.28 % Allowed : 16.62 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.02 (0.29), residues: 883 helix: 1.45 (0.72), residues: 55 sheet: 0.04 (0.28), residues: 341 loop : -0.12 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.009 0.001 TYR A 465 PHE 0.013 0.001 PHE L 209 TRP 0.006 0.001 TRP B 100A HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7100) covalent geometry : angle 0.55127 ( 9637) SS BOND : bond 0.00298 ( 11) SS BOND : angle 0.65830 ( 22) hydrogen bonds : bond 0.03266 ( 254) hydrogen bonds : angle 6.02598 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6743 (pmm) REVERT: A 286 TRP cc_start: 0.8455 (t60) cc_final: 0.8042 (t60) REVERT: B 13 GLN cc_start: 0.8091 (mp10) cc_final: 0.7738 (mp10) REVERT: H 6 GLU cc_start: 0.8461 (mp0) cc_final: 0.8025 (mp0) REVERT: H 142 VAL cc_start: 0.9205 (m) cc_final: 0.8846 (p) REVERT: L 167 ASP cc_start: 0.7599 (t70) cc_final: 0.6176 (m-30) outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 0.1990 time to fit residues: 36.6601 Evaluate side-chains 127 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114860 restraints weight = 29524.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119238 restraints weight = 16124.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122204 restraints weight = 10618.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124120 restraints weight = 7865.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125390 restraints weight = 6386.973| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7111 Z= 0.171 Angle : 0.574 7.819 9659 Z= 0.297 Chirality : 0.043 0.148 1091 Planarity : 0.003 0.032 1219 Dihedral : 4.856 18.958 970 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.66 % Allowed : 17.01 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.19 (0.29), residues: 883 helix: 1.24 (0.72), residues: 55 sheet: -0.06 (0.28), residues: 334 loop : -0.24 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.016 0.002 TYR L 49 PHE 0.012 0.002 PHE L 209 TRP 0.009 0.002 TRP B 100A HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 7100) covalent geometry : angle 0.57269 ( 9637) SS BOND : bond 0.00359 ( 11) SS BOND : angle 0.86155 ( 22) hydrogen bonds : bond 0.03473 ( 254) hydrogen bonds : angle 6.05713 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.8478 (t60) cc_final: 0.8039 (t60) REVERT: B 13 GLN cc_start: 0.8090 (mp10) cc_final: 0.7734 (mp10) REVERT: H 6 GLU cc_start: 0.8492 (mp0) cc_final: 0.8052 (mp0) REVERT: H 142 VAL cc_start: 0.9215 (m) cc_final: 0.8837 (p) REVERT: L 167 ASP cc_start: 0.7622 (t70) cc_final: 0.6159 (m-30) REVERT: L 170 ASP cc_start: 0.6948 (t0) cc_final: 0.6579 (t0) outliers start: 13 outliers final: 10 residues processed: 128 average time/residue: 0.1826 time to fit residues: 31.5247 Evaluate side-chains 130 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 50 optimal weight: 0.2980 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.142803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116546 restraints weight = 29197.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121005 restraints weight = 15836.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123982 restraints weight = 10408.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125843 restraints weight = 7722.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127212 restraints weight = 6275.226| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7111 Z= 0.114 Angle : 0.542 7.820 9659 Z= 0.278 Chirality : 0.042 0.152 1091 Planarity : 0.003 0.030 1219 Dihedral : 4.684 18.258 970 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.02 % Allowed : 17.39 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.11 (0.29), residues: 883 helix: 1.44 (0.72), residues: 55 sheet: -0.02 (0.28), residues: 340 loop : -0.20 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.010 0.001 TYR A 465 PHE 0.012 0.001 PHE L 209 TRP 0.006 0.001 TRP B 100A HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7100) covalent geometry : angle 0.54126 ( 9637) SS BOND : bond 0.00330 ( 11) SS BOND : angle 0.66152 ( 22) hydrogen bonds : bond 0.03133 ( 254) hydrogen bonds : angle 5.85851 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLU cc_start: 0.8127 (tt0) cc_final: 0.7861 (mt-10) REVERT: B 13 GLN cc_start: 0.8084 (mp10) cc_final: 0.7731 (mp10) REVERT: H 6 GLU cc_start: 0.8464 (mp0) cc_final: 0.8048 (mp0) REVERT: L 167 ASP cc_start: 0.7552 (t70) cc_final: 0.6029 (m-30) REVERT: L 170 ASP cc_start: 0.6868 (t0) cc_final: 0.6421 (t0) outliers start: 8 outliers final: 6 residues processed: 134 average time/residue: 0.1766 time to fit residues: 32.0469 Evaluate side-chains 129 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN B 105 GLN L 3 GLN L 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114787 restraints weight = 29760.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119277 restraints weight = 16123.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122282 restraints weight = 10644.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124254 restraints weight = 7924.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125423 restraints weight = 6416.769| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7111 Z= 0.155 Angle : 0.559 7.695 9659 Z= 0.289 Chirality : 0.043 0.155 1091 Planarity : 0.003 0.032 1219 Dihedral : 4.716 18.095 970 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.41 % Allowed : 16.62 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.22 (0.29), residues: 883 helix: 1.31 (0.73), residues: 55 sheet: -0.08 (0.29), residues: 333 loop : -0.27 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.014 0.001 TYR L 49 PHE 0.014 0.002 PHE L 209 TRP 0.008 0.001 TRP B 100A HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7100) covalent geometry : angle 0.55831 ( 9637) SS BOND : bond 0.00332 ( 11) SS BOND : angle 0.75148 ( 22) hydrogen bonds : bond 0.03296 ( 254) hydrogen bonds : angle 5.92488 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLU cc_start: 0.8147 (tt0) cc_final: 0.7901 (mt-10) REVERT: B 13 GLN cc_start: 0.8101 (mp10) cc_final: 0.7877 (mp10) REVERT: H 6 GLU cc_start: 0.8458 (mp0) cc_final: 0.8030 (mp0) REVERT: L 167 ASP cc_start: 0.7586 (t70) cc_final: 0.5991 (m-30) REVERT: L 170 ASP cc_start: 0.6914 (t0) cc_final: 0.6468 (t0) outliers start: 11 outliers final: 10 residues processed: 136 average time/residue: 0.1759 time to fit residues: 32.4935 Evaluate side-chains 133 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121546 restraints weight = 29778.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126391 restraints weight = 16853.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129609 restraints weight = 11414.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131595 restraints weight = 8644.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133046 restraints weight = 7097.468| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7111 Z= 0.134 Angle : 0.548 7.702 9659 Z= 0.282 Chirality : 0.042 0.155 1091 Planarity : 0.003 0.031 1219 Dihedral : 4.667 17.643 970 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.02 % Allowed : 17.65 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.23 (0.29), residues: 883 helix: 1.33 (0.73), residues: 55 sheet: -0.09 (0.29), residues: 333 loop : -0.27 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.012 0.001 TYR A 465 PHE 0.013 0.001 PHE L 209 TRP 0.007 0.001 TRP B 100A HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7100) covalent geometry : angle 0.54793 ( 9637) SS BOND : bond 0.00324 ( 11) SS BOND : angle 0.69902 ( 22) hydrogen bonds : bond 0.03147 ( 254) hydrogen bonds : angle 5.84670 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLU cc_start: 0.8128 (tt0) cc_final: 0.7882 (mt-10) REVERT: H 6 GLU cc_start: 0.8434 (mp0) cc_final: 0.8033 (mp0) REVERT: H 212 GLU cc_start: 0.7383 (pt0) cc_final: 0.7141 (pt0) outliers start: 8 outliers final: 7 residues processed: 135 average time/residue: 0.1983 time to fit residues: 35.8933 Evaluate side-chains 132 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 105 GLN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122104 restraints weight = 29728.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127059 restraints weight = 16619.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130266 restraints weight = 11121.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132338 restraints weight = 8378.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133561 restraints weight = 6853.968| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7111 Z= 0.119 Angle : 0.545 7.753 9659 Z= 0.279 Chirality : 0.042 0.156 1091 Planarity : 0.003 0.031 1219 Dihedral : 4.566 17.657 970 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.90 % Allowed : 17.90 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.17 (0.29), residues: 883 helix: 1.43 (0.74), residues: 55 sheet: -0.10 (0.29), residues: 340 loop : -0.20 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.011 0.001 TYR A 465 PHE 0.013 0.001 PHE L 209 TRP 0.006 0.001 TRP L 148 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7100) covalent geometry : angle 0.54509 ( 9637) SS BOND : bond 0.00312 ( 11) SS BOND : angle 0.63734 ( 22) hydrogen bonds : bond 0.03006 ( 254) hydrogen bonds : angle 5.73289 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.80 seconds wall clock time: 48 minutes 49.62 seconds (2929.62 seconds total)