Starting phenix.real_space_refine on Sat May 17 06:58:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vww_43604/05_2025/8vww_43604.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vww_43604/05_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_43604/05_2025/8vww_43604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vww_43604/05_2025/8vww_43604.map" model { file = "/net/cci-nas-00/data/ceres_data/8vww_43604/05_2025/8vww_43604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vww_43604/05_2025/8vww_43604.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.72, per 1000 atoms: 0.63 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: 3.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.42 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: 5.48 Time building geometry restraints manager: 4.20 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.220 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.820 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.360 ------------------------------------------------------------------------------- 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 : 4.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.005 TRP B 100A HIS 0.009 0.003 HIS A 453 PHE 0.015 0.002 PHE A 408 TYR 0.035 0.005 TYR C 87 ARG 0.014 0.002 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.25068 ( 254) hydrogen bonds : angle 9.84470 ( 660) SS BOND : bond 0.00382 ( 11) SS BOND : angle 1.32899 ( 22) covalent geometry : bond 0.00342 ( 7100) covalent geometry : angle 0.63428 ( 9637) *********************** 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 : 1.004 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: symmetry clash REVERT: A 286 TRP cc_start: 0.8376 (t60) cc_final: 0.7900 (t60) REVERT: A 480 THR cc_start: 0.8008 (m) cc_final: 0.7795 (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: 0.8565 (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: 0.7898 (m-80) REVERT: H 199 ASN cc_start: 0.8846 (t0) cc_final: 0.8636 (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: 0.8377 (t80) REVERT: L 145 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7939 (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: 0.5068 time to fit residues: 148.1898 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 : 1.150 ------------------------------------------------------------------------------- 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 73 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 422 GLN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119002 restraints weight = 28312.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123524 restraints weight = 15488.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126624 restraints weight = 10128.844| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7111 Z= 0.251 Angle : 0.720 8.159 9659 Z= 0.383 Chirality : 0.046 0.161 1091 Planarity : 0.004 0.035 1219 Dihedral : 6.387 49.610 979 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.69 % Allowed : 13.17 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.28), residues: 883 helix: 0.35 (0.68), residues: 53 sheet: -0.09 (0.28), residues: 342 loop : -0.52 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 154 HIS 0.006 0.002 HIS A 456 PHE 0.016 0.002 PHE A 321 TYR 0.019 0.002 TYR A 465 ARG 0.007 0.001 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 254) hydrogen bonds : angle 7.40223 ( 660) SS BOND : bond 0.00571 ( 11) SS BOND : angle 1.21761 ( 22) covalent geometry : bond 0.00576 ( 7100) covalent geometry : angle 0.71839 ( 9637) *********************** 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 176 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.127 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: A 251 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6670 (pmm) REVERT: A 286 TRP cc_start: 0.8546 (t60) cc_final: 0.8118 (t60) REVERT: B 13 GLN cc_start: 0.8267 (mp10) cc_final: 0.7879 (mp10) REVERT: C 18 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5526 (ttt-90) REVERT: C 39 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6767 (mtpt) REVERT: H 6 GLU cc_start: 0.8583 (mp0) cc_final: 0.8258 (mp0) REVERT: H 199 ASN cc_start: 0.8909 (t0) cc_final: 0.8699 (t0) REVERT: L 92 TYR cc_start: 0.8675 (t80) cc_final: 0.8462 (t80) outliers start: 21 outliers final: 9 residues processed: 165 average time/residue: 0.4421 time to fit residues: 96.4350 Evaluate side-chains 139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 378 THR 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 39 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN H 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118623 restraints weight = 28552.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123558 restraints weight = 14707.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126851 restraints weight = 9300.976| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7111 Z= 0.138 Angle : 0.601 7.985 9659 Z= 0.311 Chirality : 0.043 0.157 1091 Planarity : 0.004 0.034 1219 Dihedral : 5.670 47.859 976 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.79 % Allowed : 15.22 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 883 helix: 1.05 (0.69), residues: 55 sheet: 0.00 (0.27), residues: 355 loop : -0.32 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 154 HIS 0.004 0.001 HIS L 198 PHE 0.008 0.001 PHE C 83 TYR 0.013 0.002 TYR L 87 ARG 0.006 0.001 ARG L 108 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 254) hydrogen bonds : angle 6.76013 ( 660) SS BOND : bond 0.00318 ( 11) SS BOND : angle 0.77336 ( 22) covalent geometry : bond 0.00321 ( 7100) covalent geometry : angle 0.60034 ( 9637) *********************** 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 150 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.084 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: 0.7007 (OUTLIER) cc_final: 0.6712 (pmm) REVERT: A 286 TRP cc_start: 0.8410 (t60) cc_final: 0.7985 (t60) REVERT: H 6 GLU cc_start: 0.8621 (mp0) cc_final: 0.8193 (mp0) REVERT: H 199 ASN cc_start: 0.8861 (t0) cc_final: 0.8645 (t0) REVERT: L 167 ASP cc_start: 0.7646 (t70) cc_final: 0.6685 (m-30) REVERT: L 170 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7505 (m-30) outliers start: 14 outliers final: 6 residues processed: 145 average time/residue: 0.4088 time to fit residues: 79.1985 Evaluate side-chains 140 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.141442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115038 restraints weight = 28869.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119601 restraints weight = 15418.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122664 restraints weight = 10042.871| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7111 Z= 0.188 Angle : 0.608 8.355 9659 Z= 0.317 Chirality : 0.043 0.151 1091 Planarity : 0.004 0.048 1219 Dihedral : 5.261 21.921 970 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.92 % Allowed : 15.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.29), residues: 883 helix: 1.02 (0.70), residues: 55 sheet: -0.01 (0.28), residues: 342 loop : -0.32 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 100A HIS 0.004 0.001 HIS A 456 PHE 0.016 0.002 PHE L 209 TYR 0.015 0.002 TYR L 49 ARG 0.006 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 254) hydrogen bonds : angle 6.55317 ( 660) SS BOND : bond 0.00344 ( 11) SS BOND : angle 0.89558 ( 22) covalent geometry : bond 0.00437 ( 7100) covalent geometry : angle 0.60703 ( 9637) *********************** 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 145 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.130 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: 0.7112 (OUTLIER) cc_final: 0.6848 (pmm) REVERT: A 286 TRP cc_start: 0.8444 (t60) cc_final: 0.7982 (t60) REVERT: C 70 ASP cc_start: 0.7440 (t70) cc_final: 0.7183 (m-30) REVERT: C 92 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8243 (t0) REVERT: H 6 GLU cc_start: 0.8577 (mp0) cc_final: 0.8177 (mp0) REVERT: H 199 ASN cc_start: 0.8855 (t0) cc_final: 0.8642 (t0) REVERT: L 167 ASP cc_start: 0.7683 (t70) cc_final: 0.6507 (m-30) REVERT: L 170 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7406 (m-30) outliers start: 15 outliers final: 10 residues processed: 139 average time/residue: 0.3879 time to fit residues: 73.4268 Evaluate side-chains 138 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS 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 92 ASN Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 178 THR 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 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 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 248 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 = 0.3725 r_free = 0.3725 target = 0.143258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117583 restraints weight = 28637.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122188 restraints weight = 15042.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125249 restraints weight = 9603.560| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7111 Z= 0.143 Angle : 0.568 7.505 9659 Z= 0.295 Chirality : 0.043 0.151 1091 Planarity : 0.003 0.027 1219 Dihedral : 5.012 20.356 970 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.05 % Allowed : 16.88 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.29), residues: 883 helix: 1.34 (0.70), residues: 55 sheet: -0.01 (0.28), residues: 336 loop : -0.20 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 154 HIS 0.008 0.001 HIS L 198 PHE 0.012 0.001 PHE L 209 TYR 0.013 0.002 TYR B 79 ARG 0.004 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 254) hydrogen bonds : angle 6.22549 ( 660) SS BOND : bond 0.00326 ( 11) SS BOND : angle 0.79797 ( 22) covalent geometry : bond 0.00332 ( 7100) covalent geometry : angle 0.56765 ( 9637) *********************** 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 150 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.080 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: 0.7069 (OUTLIER) cc_final: 0.6832 (pmm) REVERT: A 286 TRP cc_start: 0.8406 (t60) cc_final: 0.7950 (t60) REVERT: B 13 GLN cc_start: 0.8039 (mp10) cc_final: 0.7717 (mp10) REVERT: C 39 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6954 (mtpt) REVERT: H 6 GLU cc_start: 0.8561 (mp0) cc_final: 0.8113 (mp0) REVERT: H 199 ASN cc_start: 0.8834 (t0) cc_final: 0.8623 (t0) REVERT: L 167 ASP cc_start: 0.7763 (t70) cc_final: 0.6348 (m-30) REVERT: L 170 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7456 (m-30) outliers start: 16 outliers final: 10 residues processed: 143 average time/residue: 0.3986 time to fit residues: 76.4486 Evaluate side-chains 140 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 11 LEU 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 112 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN C 92 ASN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115950 restraints weight = 28877.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120836 restraints weight = 14928.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124018 restraints weight = 9498.797| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7111 Z= 0.140 Angle : 0.575 7.762 9659 Z= 0.294 Chirality : 0.043 0.151 1091 Planarity : 0.003 0.037 1219 Dihedral : 4.880 20.096 970 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.05 % Allowed : 17.14 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.29), residues: 883 helix: 1.42 (0.72), residues: 55 sheet: -0.01 (0.29), residues: 334 loop : -0.21 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 100A HIS 0.004 0.001 HIS L 198 PHE 0.012 0.001 PHE L 209 TYR 0.013 0.001 TYR L 49 ARG 0.004 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 254) hydrogen bonds : angle 6.07104 ( 660) SS BOND : bond 0.00295 ( 11) SS BOND : angle 0.71512 ( 22) covalent geometry : bond 0.00331 ( 7100) covalent geometry : angle 0.57435 ( 9637) *********************** 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 143 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.134 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: A 251 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6823 (pmm) REVERT: A 286 TRP cc_start: 0.8456 (t60) cc_final: 0.8013 (t60) REVERT: B 13 GLN cc_start: 0.8045 (mp10) cc_final: 0.7665 (mp10) REVERT: H 6 GLU cc_start: 0.8548 (mp0) cc_final: 0.8071 (mp0) REVERT: H 142 VAL cc_start: 0.9208 (m) cc_final: 0.8840 (p) REVERT: L 167 ASP cc_start: 0.7735 (t70) cc_final: 0.6235 (m-30) REVERT: L 170 ASP cc_start: 0.7882 (m-30) cc_final: 0.7673 (t0) outliers start: 16 outliers final: 11 residues processed: 139 average time/residue: 0.4082 time to fit residues: 76.0116 Evaluate side-chains 135 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 72 optimal weight: 0.0170 chunk 49 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.142713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116039 restraints weight = 29353.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120520 restraints weight = 15880.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123491 restraints weight = 10470.019| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5271 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= 0.149 Angle : 0.561 7.743 9659 Z= 0.289 Chirality : 0.043 0.155 1091 Planarity : 0.003 0.037 1219 Dihedral : 4.829 20.452 970 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.66 % Allowed : 17.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.29), residues: 883 helix: 1.52 (0.72), residues: 55 sheet: -0.06 (0.29), residues: 334 loop : -0.22 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 100A HIS 0.003 0.001 HIS L 198 PHE 0.011 0.001 PHE L 209 TYR 0.013 0.001 TYR L 49 ARG 0.003 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 254) hydrogen bonds : angle 6.02414 ( 660) SS BOND : bond 0.00341 ( 11) SS BOND : angle 0.77700 ( 22) covalent geometry : bond 0.00351 ( 7100) covalent geometry : angle 0.56033 ( 9637) *********************** 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 139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.204 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: 0.7095 (OUTLIER) cc_final: 0.6885 (pmm) REVERT: B 13 GLN cc_start: 0.8086 (mp10) cc_final: 0.7704 (mp10) REVERT: H 6 GLU cc_start: 0.8502 (mp0) cc_final: 0.8048 (mp0) REVERT: H 142 VAL cc_start: 0.9223 (m) cc_final: 0.8844 (p) REVERT: L 167 ASP cc_start: 0.7673 (t70) cc_final: 0.6175 (m-30) outliers start: 13 outliers final: 11 residues processed: 136 average time/residue: 0.4069 time to fit residues: 74.2530 Evaluate side-chains 132 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 HIS 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 H residue 138 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 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114580 restraints weight = 29717.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118972 restraints weight = 16211.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121991 restraints weight = 10815.204| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7111 Z= 0.180 Angle : 0.583 7.761 9659 Z= 0.301 Chirality : 0.043 0.157 1091 Planarity : 0.003 0.036 1219 Dihedral : 4.882 21.292 970 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.79 % Allowed : 16.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.29), residues: 883 helix: 1.45 (0.73), residues: 55 sheet: -0.17 (0.29), residues: 334 loop : -0.37 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 100A HIS 0.003 0.001 HIS L 189 PHE 0.011 0.002 PHE H 146 TYR 0.015 0.002 TYR L 49 ARG 0.003 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 254) hydrogen bonds : angle 6.06835 ( 660) SS BOND : bond 0.00340 ( 11) SS BOND : angle 0.84626 ( 22) covalent geometry : bond 0.00421 ( 7100) covalent geometry : angle 0.58200 ( 9637) *********************** 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 142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.133 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: B 13 GLN cc_start: 0.8102 (mp10) cc_final: 0.7729 (mp10) REVERT: H 6 GLU cc_start: 0.8512 (mp0) cc_final: 0.8054 (mp0) REVERT: H 142 VAL cc_start: 0.9227 (m) cc_final: 0.8847 (p) REVERT: L 167 ASP cc_start: 0.7659 (t70) cc_final: 0.6126 (m-30) REVERT: L 170 ASP cc_start: 0.7159 (t0) cc_final: 0.6657 (t0) outliers start: 14 outliers final: 11 residues processed: 139 average time/residue: 0.3979 time to fit residues: 75.2002 Evaluate side-chains 135 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 99 SER 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 L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.116208 restraints weight = 29491.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120632 restraints weight = 16210.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123510 restraints weight = 10773.095| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7111 Z= 0.149 Angle : 0.569 7.804 9659 Z= 0.292 Chirality : 0.043 0.159 1091 Planarity : 0.003 0.035 1219 Dihedral : 4.821 20.075 970 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.92 % Allowed : 17.14 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.29), residues: 883 helix: 1.54 (0.74), residues: 55 sheet: -0.14 (0.29), residues: 331 loop : -0.39 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 100A HIS 0.003 0.001 HIS L 198 PHE 0.011 0.001 PHE L 209 TYR 0.013 0.001 TYR L 49 ARG 0.006 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 254) hydrogen bonds : angle 5.97673 ( 660) SS BOND : bond 0.00323 ( 11) SS BOND : angle 0.76696 ( 22) covalent geometry : bond 0.00350 ( 7100) covalent geometry : angle 0.56848 ( 9637) *********************** 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 142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.104 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: B 31 SER cc_start: 0.7959 (p) cc_final: 0.7668 (t) REVERT: C 42 ARG cc_start: 0.7737 (tpp80) cc_final: 0.7345 (tpp80) REVERT: H 6 GLU cc_start: 0.8500 (mp0) cc_final: 0.8053 (mp0) REVERT: L 167 ASP cc_start: 0.7615 (t70) cc_final: 0.6014 (m-30) REVERT: L 170 ASP cc_start: 0.7067 (t0) cc_final: 0.6639 (t0) outliers start: 15 outliers final: 14 residues processed: 138 average time/residue: 0.4169 time to fit residues: 77.6432 Evaluate side-chains 139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS 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 82 MET Chi-restraints excluded: chain B residue 92 CYS 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 H residue 138 LEU 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 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 72 optimal weight: 0.0370 chunk 8 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.142836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116137 restraints weight = 29500.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120688 restraints weight = 15883.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123725 restraints weight = 10400.082| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7111 Z= 0.129 Angle : 0.568 7.860 9659 Z= 0.290 Chirality : 0.043 0.156 1091 Planarity : 0.003 0.034 1219 Dihedral : 4.741 19.370 970 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.53 % Allowed : 18.03 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.29), residues: 883 helix: 1.63 (0.74), residues: 55 sheet: -0.15 (0.29), residues: 334 loop : -0.32 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 154 HIS 0.003 0.001 HIS L 198 PHE 0.024 0.001 PHE H 122 TYR 0.011 0.001 TYR A 465 ARG 0.006 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 254) hydrogen bonds : angle 5.89533 ( 660) SS BOND : bond 0.00308 ( 11) SS BOND : angle 0.71345 ( 22) covalent geometry : bond 0.00306 ( 7100) covalent geometry : angle 0.56770 ( 9637) ********************** 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 140 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.075 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: 0.8144 (tt0) cc_final: 0.7905 (mt-10) REVERT: B 31 SER cc_start: 0.7778 (p) cc_final: 0.7501 (t) REVERT: C 42 ARG cc_start: 0.7730 (tpp80) cc_final: 0.7348 (tpp80) REVERT: H 6 GLU cc_start: 0.8505 (mp0) cc_final: 0.8058 (mp0) outliers start: 12 outliers final: 12 residues processed: 137 average time/residue: 0.4054 time to fit residues: 74.3212 Evaluate side-chains 138 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS 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 82 MET Chi-restraints excluded: chain B residue 92 CYS 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 138 LEU 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 9 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 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 476 ASN B 32 ASN B 105 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 = 0.3742 r_free = 0.3742 target = 0.142121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115272 restraints weight = 29534.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119794 restraints weight = 16025.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122795 restraints weight = 10603.261| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7111 Z= 0.155 Angle : 0.571 7.844 9659 Z= 0.293 Chirality : 0.043 0.156 1091 Planarity : 0.003 0.035 1219 Dihedral : 4.782 20.309 970 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.79 % Allowed : 17.65 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 883 helix: 1.54 (0.73), residues: 55 sheet: -0.13 (0.29), residues: 330 loop : -0.38 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 100A HIS 0.003 0.001 HIS L 198 PHE 0.016 0.001 PHE H 122 TYR 0.014 0.001 TYR L 49 ARG 0.005 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 254) hydrogen bonds : angle 5.90643 ( 660) SS BOND : bond 0.00301 ( 11) SS BOND : angle 0.75572 ( 22) covalent geometry : bond 0.00366 ( 7100) covalent geometry : angle 0.57003 ( 9637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4972.22 seconds wall clock time: 86 minutes 47.24 seconds (5207.24 seconds total)