Starting phenix.real_space_refine on Fri Jul 25 12:28:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dk9_46948/07_2025/9dk9_46948.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dk9_46948/07_2025/9dk9_46948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dk9_46948/07_2025/9dk9_46948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dk9_46948/07_2025/9dk9_46948.map" model { file = "/net/cci-nas-00/data/ceres_data/9dk9_46948/07_2025/9dk9_46948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dk9_46948/07_2025/9dk9_46948.cif" } resolution = 2.68 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2474 2.51 5 N 657 2.21 5 O 659 1.98 5 H 3844 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7660 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 7660 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 30, 'TRANS': 486} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 4.27, per 1000 atoms: 0.56 Number of scatterers: 7660 At special positions: 0 Unit cell: (111.055, 69.305, 70.14, 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 26 16.00 O 659 8.00 N 657 7.00 C 2474 6.00 H 3844 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 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: 1.96 Conformation dependent library (CDL) restraints added in 701.9 milliseconds 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 81.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 37 removed outlier: 3.686A pdb=" N VAL A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Proline residue: A 27 - end of helix removed outlier: 3.840A pdb=" N TRP A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.574A pdb=" N GLN A 60 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.920A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.501A pdb=" N ASP A 100 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 168 removed outlier: 3.520A pdb=" N TYR A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.837A pdb=" N ALA A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.599A pdb=" N GLY A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 253 removed outlier: 3.534A pdb=" N VAL A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.382A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.923A pdb=" N GLY A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.612A pdb=" N THR A 339 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 370 removed outlier: 4.010A pdb=" N PHE A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.100A pdb=" N LEU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 375' Processing helix chain 'A' and resid 377 through 403 removed outlier: 3.534A pdb=" N LEU A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 3.870A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.858A pdb=" N THR A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 3.681A pdb=" N ILE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 486 Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.126A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.027A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.526A pdb=" N GLY A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 251 hydrogen bonds defined for protein. 726 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: 2.70 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3835 1.03 - 1.23: 10 1.23 - 1.42: 1584 1.42 - 1.62: 2280 1.62 - 1.81: 39 Bond restraints: 7748 Sorted by residual: bond pdb=" CB GLN A 17 " pdb=" CG GLN A 17 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 9.01e-01 bond pdb=" CG GLN A 17 " pdb=" CD GLN A 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.74e-01 bond pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta sigma weight residual 1.463 1.457 0.006 6.90e-03 2.10e+04 7.19e-01 bond pdb=" CA VAL A 26 " pdb=" CB VAL A 26 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 6.58e-01 bond pdb=" CB GLN A 97 " pdb=" CG GLN A 97 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.05e-01 ... (remaining 7743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 12697 1.01 - 2.03: 1218 2.03 - 3.04: 81 3.04 - 4.06: 31 4.06 - 5.07: 5 Bond angle restraints: 14032 Sorted by residual: angle pdb=" C GLU A 223 " pdb=" N TRP A 224 " pdb=" CA TRP A 224 " ideal model delta sigma weight residual 120.58 117.01 3.57 1.71e+00 3.42e-01 4.37e+00 angle pdb=" CB GLN A 17 " pdb=" CG GLN A 17 " pdb=" CD GLN A 17 " ideal model delta sigma weight residual 112.60 116.11 -3.51 1.70e+00 3.46e-01 4.27e+00 angle pdb=" C LYS A 145 " pdb=" CA LYS A 145 " pdb=" CB LYS A 145 " ideal model delta sigma weight residual 113.57 110.41 3.16 1.57e+00 4.06e-01 4.06e+00 angle pdb=" CA GLN A 97 " pdb=" CB GLN A 97 " pdb=" CG GLN A 97 " ideal model delta sigma weight residual 114.10 118.11 -4.01 2.00e+00 2.50e-01 4.01e+00 angle pdb=" CA ARG A 284 " pdb=" CB ARG A 284 " pdb=" CG ARG A 284 " ideal model delta sigma weight residual 114.10 117.99 -3.89 2.00e+00 2.50e-01 3.79e+00 ... (remaining 14027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3131 17.35 - 34.69: 322 34.69 - 52.04: 153 52.04 - 69.38: 42 69.38 - 86.73: 14 Dihedral angle restraints: 3662 sinusoidal: 1959 harmonic: 1703 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -158.36 72.36 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " pdb=" NE ARG A 256 " pdb=" CZ ARG A 256 " ideal model delta sinusoidal sigma weight residual -90.00 -39.75 -50.25 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CA GLN A 87 " pdb=" CB GLN A 87 " pdb=" CG GLN A 87 " pdb=" CD GLN A 87 " ideal model delta sinusoidal sigma weight residual -180.00 -122.52 -57.48 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 422 0.026 - 0.052: 122 0.052 - 0.078: 64 0.078 - 0.105: 26 0.105 - 0.131: 4 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA VAL A 63 " pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CB VAL A 63 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL A 121 " pdb=" N VAL A 121 " pdb=" C VAL A 121 " pdb=" CB VAL A 121 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL A 44 " pdb=" N VAL A 44 " pdb=" C VAL A 44 " pdb=" CB VAL A 44 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 635 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 17 " -0.009 2.00e-02 2.50e+03 1.83e-02 5.01e+00 pdb=" CD GLN A 17 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN A 17 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN A 17 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN A 17 " -0.007 2.00e-02 2.50e+03 pdb="HE22 GLN A 17 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 256 " 0.124 9.50e-02 1.11e+02 4.16e-02 2.03e+00 pdb=" NE ARG A 256 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 256 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 256 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 256 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 256 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 256 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 256 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 256 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 26 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 27 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.019 5.00e-02 4.00e+02 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 133 2.11 - 2.73: 12835 2.73 - 3.35: 21951 3.35 - 3.98: 25744 3.98 - 4.60: 40723 Nonbonded interactions: 101386 Sorted by model distance: nonbonded pdb=" OE1 GLN A 97 " pdb=" H GLN A 97 " model vdw 1.487 2.450 nonbonded pdb=" OE1 GLU A 70 " pdb=" H GLU A 70 " model vdw 1.516 2.450 nonbonded pdb=" O GLN A 17 " pdb=" HG1 THR A 21 " model vdw 1.614 2.450 nonbonded pdb=" O TRP A 278 " pdb="HH22 ARG A 301 " model vdw 1.694 2.450 nonbonded pdb=" OD1 ASN A 377 " pdb=" H LEU A 380 " model vdw 1.712 2.450 ... (remaining 101381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.100 Find NCS groups from input model: 0.060 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 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 0.028 3906 Z= 0.124 Angle : 0.557 5.071 5341 Z= 0.293 Chirality : 0.035 0.131 638 Planarity : 0.005 0.054 675 Dihedral : 17.614 86.730 1345 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.78 % Allowed : 34.64 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.38), residues: 515 helix: 1.53 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.96 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 285 HIS 0.006 0.001 HIS A 86 PHE 0.017 0.001 PHE A 243 TYR 0.009 0.001 TYR A 275 ARG 0.006 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.17192 ( 251) hydrogen bonds : angle 5.29673 ( 726) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.46090 ( 4) covalent geometry : bond 0.00258 ( 3904) covalent geometry : angle 0.55711 ( 5337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.570 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: A 34 GLN cc_start: 0.7856 (tp40) cc_final: 0.7559 (mm110) REVERT: A 36 MET cc_start: 0.7777 (tpp) cc_final: 0.7548 (mmm) REVERT: A 147 MET cc_start: 0.6352 (ttp) cc_final: 0.5882 (tpt) REVERT: A 178 TRP cc_start: 0.6576 (t-100) cc_final: 0.5900 (t60) REVERT: A 242 SER cc_start: 0.6914 (OUTLIER) cc_final: 0.6541 (t) REVERT: A 257 ASP cc_start: 0.7065 (m-30) cc_final: 0.6659 (t70) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 1.5213 time to fit residues: 99.4030 Evaluate side-chains 59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 242 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.235372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.189864 restraints weight = 12370.193| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.57 r_work: 0.4195 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3906 Z= 0.148 Angle : 0.567 4.928 5341 Z= 0.296 Chirality : 0.037 0.138 638 Planarity : 0.005 0.046 675 Dihedral : 4.626 50.908 556 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.47 % Allowed : 29.43 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.38), residues: 515 helix: 1.49 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.57 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 50 HIS 0.006 0.001 HIS A 86 PHE 0.011 0.001 PHE A 362 TYR 0.013 0.002 TYR A 275 ARG 0.004 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.05395 ( 251) hydrogen bonds : angle 4.23471 ( 726) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.49070 ( 4) covalent geometry : bond 0.00305 ( 3904) covalent geometry : angle 0.56742 ( 5337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7714 (mm110) REVERT: A 142 GLN cc_start: 0.7990 (tt0) cc_final: 0.7638 (tt0) REVERT: A 147 MET cc_start: 0.7143 (ttp) cc_final: 0.6703 (tpp) outliers start: 21 outliers final: 5 residues processed: 72 average time/residue: 1.3514 time to fit residues: 103.0315 Evaluate side-chains 61 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 378 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.223930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.178326 restraints weight = 12474.430| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.48 r_work: 0.4085 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 3906 Z= 0.213 Angle : 0.624 4.933 5341 Z= 0.329 Chirality : 0.040 0.139 638 Planarity : 0.006 0.043 675 Dihedral : 4.834 51.564 555 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 6.51 % Allowed : 26.82 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.36), residues: 515 helix: 0.87 (0.27), residues: 369 sheet: -3.78 (1.28), residues: 10 loop : -0.97 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 357 HIS 0.009 0.002 HIS A 86 PHE 0.016 0.002 PHE A 362 TYR 0.014 0.002 TYR A 275 ARG 0.005 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.06214 ( 251) hydrogen bonds : angle 4.30407 ( 726) SS BOND : bond 0.00451 ( 2) SS BOND : angle 0.22477 ( 4) covalent geometry : bond 0.00495 ( 3904) covalent geometry : angle 0.62467 ( 5337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3236 (OUTLIER) cc_final: 0.2784 (tt) REVERT: A 147 MET cc_start: 0.7632 (ttp) cc_final: 0.6933 (tpp) REVERT: A 242 SER cc_start: 0.7542 (m) cc_final: 0.7196 (t) REVERT: A 279 LEU cc_start: 0.4893 (mt) cc_final: 0.3967 (pp) outliers start: 25 outliers final: 8 residues processed: 80 average time/residue: 1.1174 time to fit residues: 95.6178 Evaluate side-chains 66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.224749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.179577 restraints weight = 12422.951| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.45 r_work: 0.4099 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3906 Z= 0.135 Angle : 0.538 4.866 5341 Z= 0.275 Chirality : 0.036 0.129 638 Planarity : 0.004 0.043 675 Dihedral : 4.652 52.667 555 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.43 % Allowed : 28.65 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.38), residues: 515 helix: 1.19 (0.28), residues: 369 sheet: -3.80 (1.33), residues: 10 loop : -0.97 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 50 HIS 0.005 0.001 HIS A 86 PHE 0.013 0.001 PHE A 362 TYR 0.014 0.002 TYR A 275 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 251) hydrogen bonds : angle 4.07976 ( 726) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.42399 ( 4) covalent geometry : bond 0.00299 ( 3904) covalent geometry : angle 0.53782 ( 5337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3040 (OUTLIER) cc_final: 0.2607 (tt) REVERT: A 147 MET cc_start: 0.7635 (ttp) cc_final: 0.6909 (tpp) REVERT: A 224 TRP cc_start: 0.7286 (m100) cc_final: 0.6433 (m100) REVERT: A 242 SER cc_start: 0.7430 (m) cc_final: 0.7165 (t) REVERT: A 279 LEU cc_start: 0.4830 (mt) cc_final: 0.3845 (pp) outliers start: 17 outliers final: 8 residues processed: 70 average time/residue: 1.1735 time to fit residues: 88.0551 Evaluate side-chains 66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.225780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.180122 restraints weight = 12487.777| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.49 r_work: 0.4101 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.118 Angle : 0.507 4.937 5341 Z= 0.258 Chirality : 0.035 0.129 638 Planarity : 0.004 0.039 675 Dihedral : 4.523 53.683 555 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.86 % Allowed : 27.86 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.38), residues: 515 helix: 1.43 (0.28), residues: 369 sheet: -3.69 (1.25), residues: 10 loop : -0.89 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.004 0.001 HIS A 86 PHE 0.013 0.001 PHE A 362 TYR 0.012 0.001 TYR A 275 ARG 0.003 0.000 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 251) hydrogen bonds : angle 3.95035 ( 726) SS BOND : bond 0.00184 ( 2) SS BOND : angle 0.31355 ( 4) covalent geometry : bond 0.00260 ( 3904) covalent geometry : angle 0.50753 ( 5337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3145 (OUTLIER) cc_final: 0.2716 (tt) REVERT: A 147 MET cc_start: 0.7353 (ttp) cc_final: 0.6809 (tpp) REVERT: A 224 TRP cc_start: 0.7111 (m100) cc_final: 0.6340 (m100) REVERT: A 242 SER cc_start: 0.7390 (m) cc_final: 0.7134 (t) REVERT: A 279 LEU cc_start: 0.4842 (mt) cc_final: 0.3921 (pp) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 1.1053 time to fit residues: 81.8610 Evaluate side-chains 65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.0060 chunk 2 optimal weight: 0.7980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.225601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.180043 restraints weight = 12332.012| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.46 r_work: 0.4094 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.124 Angle : 0.513 4.957 5341 Z= 0.262 Chirality : 0.036 0.129 638 Planarity : 0.004 0.039 675 Dihedral : 4.482 54.494 555 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.39 % Allowed : 28.39 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.38), residues: 515 helix: 1.45 (0.28), residues: 369 sheet: -3.76 (1.20), residues: 10 loop : -0.82 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 50 HIS 0.004 0.001 HIS A 86 PHE 0.013 0.001 PHE A 362 TYR 0.013 0.001 TYR A 275 ARG 0.002 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 251) hydrogen bonds : angle 3.92574 ( 726) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.29277 ( 4) covalent geometry : bond 0.00281 ( 3904) covalent geometry : angle 0.51292 ( 5337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3253 (OUTLIER) cc_final: 0.2815 (tt) REVERT: A 147 MET cc_start: 0.7322 (ttp) cc_final: 0.6806 (tpp) REVERT: A 224 TRP cc_start: 0.7022 (m100) cc_final: 0.6346 (m100) REVERT: A 242 SER cc_start: 0.7407 (m) cc_final: 0.7153 (t) REVERT: A 279 LEU cc_start: 0.4892 (mt) cc_final: 0.3966 (pp) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 1.3288 time to fit residues: 95.4973 Evaluate side-chains 67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.225439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.179259 restraints weight = 12329.424| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.47 r_work: 0.4087 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.124 Angle : 0.506 4.948 5341 Z= 0.259 Chirality : 0.036 0.132 638 Planarity : 0.004 0.039 675 Dihedral : 4.460 55.418 555 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.69 % Allowed : 26.82 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.38), residues: 515 helix: 1.51 (0.28), residues: 370 sheet: -3.65 (1.28), residues: 10 loop : -0.81 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 50 HIS 0.004 0.001 HIS A 86 PHE 0.014 0.001 PHE A 362 TYR 0.013 0.001 TYR A 275 ARG 0.002 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 251) hydrogen bonds : angle 3.91236 ( 726) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.36961 ( 4) covalent geometry : bond 0.00282 ( 3904) covalent geometry : angle 0.50596 ( 5337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7652 (ttp) cc_final: 0.6949 (tpp) REVERT: A 224 TRP cc_start: 0.7096 (m100) cc_final: 0.6369 (m100) REVERT: A 242 SER cc_start: 0.7470 (m) cc_final: 0.7245 (t) REVERT: A 279 LEU cc_start: 0.4950 (mt) cc_final: 0.3930 (pp) outliers start: 18 outliers final: 10 residues processed: 73 average time/residue: 1.2055 time to fit residues: 94.4267 Evaluate side-chains 66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.225223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.178929 restraints weight = 12351.752| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.46 r_work: 0.4089 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.124 Angle : 0.516 4.975 5341 Z= 0.263 Chirality : 0.036 0.128 638 Planarity : 0.004 0.041 675 Dihedral : 4.454 55.840 555 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.65 % Allowed : 28.65 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.38), residues: 515 helix: 1.47 (0.28), residues: 370 sheet: -3.71 (1.28), residues: 10 loop : -0.74 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 50 HIS 0.004 0.001 HIS A 86 PHE 0.014 0.001 PHE A 362 TYR 0.013 0.001 TYR A 275 ARG 0.002 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 251) hydrogen bonds : angle 3.92982 ( 726) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.40788 ( 4) covalent geometry : bond 0.00281 ( 3904) covalent geometry : angle 0.51610 ( 5337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3365 (OUTLIER) cc_final: 0.2947 (tt) REVERT: A 147 MET cc_start: 0.7359 (ttp) cc_final: 0.6821 (tpp) REVERT: A 224 TRP cc_start: 0.6934 (m100) cc_final: 0.6279 (m100) REVERT: A 242 SER cc_start: 0.7480 (m) cc_final: 0.7230 (t) REVERT: A 279 LEU cc_start: 0.4991 (mt) cc_final: 0.4018 (pp) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 1.1846 time to fit residues: 85.3182 Evaluate side-chains 64 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.224408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.178166 restraints weight = 12361.612| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.47 r_work: 0.4077 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.132 Angle : 0.515 4.915 5341 Z= 0.265 Chirality : 0.036 0.128 638 Planarity : 0.004 0.040 675 Dihedral : 4.489 56.176 555 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.86 % Allowed : 28.91 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.39), residues: 515 helix: 1.47 (0.28), residues: 369 sheet: -3.75 (1.28), residues: 10 loop : -0.51 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 50 HIS 0.004 0.001 HIS A 86 PHE 0.014 0.001 PHE A 362 TYR 0.013 0.001 TYR A 275 ARG 0.003 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 251) hydrogen bonds : angle 3.93672 ( 726) SS BOND : bond 0.00301 ( 2) SS BOND : angle 0.43953 ( 4) covalent geometry : bond 0.00304 ( 3904) covalent geometry : angle 0.51549 ( 5337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3453 (OUTLIER) cc_final: 0.3048 (tt) REVERT: A 147 MET cc_start: 0.7657 (ttp) cc_final: 0.6953 (tpp) REVERT: A 224 TRP cc_start: 0.6977 (m100) cc_final: 0.6365 (m100) REVERT: A 242 SER cc_start: 0.7533 (m) cc_final: 0.7300 (t) REVERT: A 279 LEU cc_start: 0.5020 (mt) cc_final: 0.3979 (pp) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 1.0424 time to fit residues: 74.3109 Evaluate side-chains 65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.225688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.179487 restraints weight = 12348.357| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.46 r_work: 0.4091 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3906 Z= 0.112 Angle : 0.510 4.948 5341 Z= 0.257 Chirality : 0.035 0.129 638 Planarity : 0.004 0.041 675 Dihedral : 4.410 56.513 555 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.86 % Allowed : 28.91 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.39), residues: 515 helix: 1.59 (0.28), residues: 369 sheet: -3.64 (1.29), residues: 10 loop : -0.45 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.004 0.001 HIS A 86 PHE 0.013 0.001 PHE A 362 TYR 0.013 0.001 TYR A 275 ARG 0.003 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 251) hydrogen bonds : angle 3.86619 ( 726) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.46920 ( 4) covalent geometry : bond 0.00249 ( 3904) covalent geometry : angle 0.50957 ( 5337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7328 (ttp) cc_final: 0.6795 (tpp) REVERT: A 224 TRP cc_start: 0.6812 (m100) cc_final: 0.6269 (m100) REVERT: A 242 SER cc_start: 0.7527 (m) cc_final: 0.7283 (t) REVERT: A 278 TRP cc_start: 0.6708 (m-90) cc_final: 0.6138 (m-90) REVERT: A 279 LEU cc_start: 0.4945 (mt) cc_final: 0.3967 (pp) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 1.0796 time to fit residues: 76.6214 Evaluate side-chains 65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 6 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.224548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.178384 restraints weight = 12375.568| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.47 r_work: 0.4068 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3948 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3906 Z= 0.127 Angle : 0.517 4.935 5341 Z= 0.264 Chirality : 0.036 0.129 638 Planarity : 0.004 0.041 675 Dihedral : 3.529 17.222 552 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.34 % Allowed : 29.43 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.38), residues: 515 helix: 1.50 (0.28), residues: 370 sheet: -3.77 (1.28), residues: 10 loop : -0.57 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 50 HIS 0.004 0.001 HIS A 86 PHE 0.014 0.001 PHE A 362 TYR 0.012 0.001 TYR A 275 ARG 0.003 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 251) hydrogen bonds : angle 3.90517 ( 726) SS BOND : bond 0.00298 ( 2) SS BOND : angle 0.46873 ( 4) covalent geometry : bond 0.00291 ( 3904) covalent geometry : angle 0.51670 ( 5337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5991.03 seconds wall clock time: 103 minutes 22.82 seconds (6202.82 seconds total)