Starting phenix.real_space_refine on Wed Feb 4 00:14:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qbh_52999/02_2026/9qbh_52999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qbh_52999/02_2026/9qbh_52999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qbh_52999/02_2026/9qbh_52999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qbh_52999/02_2026/9qbh_52999.map" model { file = "/net/cci-nas-00/data/ceres_data/9qbh_52999/02_2026/9qbh_52999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qbh_52999/02_2026/9qbh_52999.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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 41 5.16 5 C 2437 2.51 5 N 702 2.21 5 O 737 1.98 5 H 3765 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7682 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 7682 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 29, 'TRANS': 478} Chain breaks: 2 Time building chain proxies: 1.55, per 1000 atoms: 0.20 Number of scatterers: 7682 At special positions: 0 Unit cell: (66.402, 89.838, 100.254, 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 41 16.00 O 737 8.00 N 702 7.00 C 2437 6.00 H 3765 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 53 " distance=2.04 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 192 " distance=2.02 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 204 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.04 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 311 " distance=2.07 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 331 " distance=2.07 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 338 " distance=2.06 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 367 " distance=2.02 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 504 " distance=2.02 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 540 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 180.9 milliseconds 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 10 sheets defined 19.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 38 through 51 removed outlier: 4.517A pdb=" N LEU A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASP A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 4.128A pdb=" N ASP A 76 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 220 through 224 removed outlier: 4.396A pdb=" N CYS A 224 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 360 through 365 Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.863A pdb=" N CYS A 26 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.600A pdb=" N LEU A 60 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA A 87 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 62 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR A 112 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A 154 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 114 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLN A 156 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 116 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.721A pdb=" N GLY A 243 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N CYS A 252 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 274 Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 376 removed outlier: 6.510A pdb=" N LEU A 410 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLN A 446 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 412 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 441 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU A 467 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 443 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS A 469 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 445 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA A 466 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N THR A 496 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 468 " --> pdb=" O THR A 496 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 534 through 536 removed outlier: 4.064A pdb=" N PHE A 534 " --> pdb=" O VAL A 541 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.14: 3765 1.14 - 1.33: 1177 1.33 - 1.52: 2014 1.52 - 1.70: 767 1.70 - 1.89: 46 Bond restraints: 7769 Sorted by residual: bond pdb=" NE1 TRP A 169 " pdb=" HE1 TRP A 169 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" OG1 THR A 27 " pdb=" HG1 THR A 27 " ideal model delta sigma weight residual 0.840 1.024 -0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" NH1 ARG A 499 " pdb="HH11 ARG A 499 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" NE1 TRP A 452 " pdb=" HE1 TRP A 452 " ideal model delta sigma weight residual 0.860 1.042 -0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" NH2 ARG A 157 " pdb="HH21 ARG A 157 " ideal model delta sigma weight residual 0.860 1.042 -0.182 2.00e-02 2.50e+03 8.26e+01 ... (remaining 7764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 18.50: 14019 18.50 - 37.01: 0 37.01 - 55.51: 0 55.51 - 74.02: 0 74.02 - 92.52: 1 Bond angle restraints: 14020 Sorted by residual: angle pdb=" HB2 ARG A 330 " pdb=" CB ARG A 330 " pdb=" HB3 ARG A 330 " ideal model delta sigma weight residual 110.00 17.48 92.52 3.00e+00 1.11e-01 9.51e+02 angle pdb=" CA ASP A 251 " pdb=" CB ASP A 251 " pdb=" CG ASP A 251 " ideal model delta sigma weight residual 112.60 121.35 -8.75 1.00e+00 1.00e+00 7.65e+01 angle pdb=" C GLY A 524 " pdb=" N PRO A 525 " pdb=" CA PRO A 525 " ideal model delta sigma weight residual 119.87 128.59 -8.72 1.04e+00 9.25e-01 7.02e+01 angle pdb=" C GLY A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta sigma weight residual 119.87 128.21 -8.34 1.04e+00 9.25e-01 6.42e+01 angle pdb=" C SER A 196 " pdb=" N PRO A 197 " pdb=" CA PRO A 197 " ideal model delta sigma weight residual 119.82 126.90 -7.08 9.80e-01 1.04e+00 5.21e+01 ... (remaining 14015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3508 17.75 - 35.50: 145 35.50 - 53.25: 58 53.25 - 71.00: 19 71.00 - 88.75: 4 Dihedral angle restraints: 3734 sinusoidal: 2056 harmonic: 1678 Sorted by residual: dihedral pdb=" CB GLU A 321 " pdb=" CG GLU A 321 " pdb=" CD GLU A 321 " pdb=" OE1 GLU A 321 " ideal model delta sinusoidal sigma weight residual 0.00 -88.75 88.75 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" C ARG A 203 " pdb=" N ARG A 203 " pdb=" CA ARG A 203 " pdb=" CB ARG A 203 " ideal model delta harmonic sigma weight residual -122.60 -115.03 -7.57 0 2.50e+00 1.60e-01 9.17e+00 dihedral pdb=" CA CYS A 342 " pdb=" CB CYS A 342 " pdb=" SG CYS A 342 " pdb=" SG CYS A 367 " ideal model delta sinusoidal sigma weight residual -73.00 -124.06 51.06 1 2.00e+01 2.50e-03 8.92e+00 ... (remaining 3731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 343 0.070 - 0.139: 179 0.139 - 0.208: 62 0.208 - 0.278: 18 0.278 - 0.347: 5 Chirality restraints: 607 Sorted by residual: chirality pdb=" CA PHE A 279 " pdb=" N PHE A 279 " pdb=" C PHE A 279 " pdb=" CB PHE A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA CYS A 540 " pdb=" N CYS A 540 " pdb=" C CYS A 540 " pdb=" CB CYS A 540 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASN A 111 " pdb=" N ASN A 111 " pdb=" C ASN A 111 " pdb=" CB ASN A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 604 not shown) Planarity restraints: 1197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 409 " 0.086 2.00e-02 2.50e+03 3.74e-02 4.20e+01 pdb=" CG TYR A 409 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 409 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 409 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 409 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR A 409 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 409 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 409 " 0.077 2.00e-02 2.50e+03 pdb=" HD1 TYR A 409 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 409 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 409 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR A 409 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 452 " -0.048 2.00e-02 2.50e+03 1.93e-02 1.49e+01 pdb=" CG TRP A 452 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 452 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 452 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 452 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP A 452 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 452 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 452 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 452 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 452 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 452 " 0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP A 452 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP A 452 " 0.020 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 452 " -0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 452 " 0.017 2.00e-02 2.50e+03 pdb=" HH2 TRP A 452 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 163 " -0.052 2.00e-02 2.50e+03 2.15e-02 1.39e+01 pdb=" CG TYR A 163 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 163 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 163 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 163 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 163 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 163 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 163 " -0.039 2.00e-02 2.50e+03 pdb=" HD1 TYR A 163 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR A 163 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR A 163 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 163 " 0.002 2.00e-02 2.50e+03 ... (remaining 1194 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.92: 244 1.92 - 2.59: 8321 2.59 - 3.26: 24441 3.26 - 3.93: 32160 3.93 - 4.60: 48269 Nonbonded interactions: 113435 Sorted by model distance: nonbonded pdb=" HH TYR A 289 " pdb=" HG SER A 305 " model vdw 1.255 2.100 nonbonded pdb=" H SER A 387 " pdb=" H ASN A 388 " model vdw 1.324 2.100 nonbonded pdb=" H SER A 413 " pdb=" H ALA A 414 " model vdw 1.346 2.100 nonbonded pdb=" HH TYR A 289 " pdb=" OG SER A 305 " model vdw 1.608 2.450 nonbonded pdb=" OE1 GLU A 325 " pdb=" H GLU A 325 " model vdw 1.635 2.450 ... (remaining 113430 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 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: 0.570 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: 0.050 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.021 0.144 4022 Z= 1.187 Angle : 1.797 10.105 5479 Z= 1.225 Chirality : 0.095 0.347 607 Planarity : 0.009 0.045 720 Dihedral : 11.255 88.747 1463 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.38), residues: 502 helix: -2.93 (0.62), residues: 38 sheet: 0.06 (0.60), residues: 57 loop : 1.35 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 188 TYR 0.078 0.011 TYR A 409 PHE 0.026 0.007 PHE A 258 TRP 0.028 0.008 TRP A 415 HIS 0.015 0.003 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.02121 ( 4004) covalent geometry : angle 1.79274 ( 5443) SS BOND : bond 0.01614 ( 18) SS BOND : angle 2.40578 ( 36) hydrogen bonds : bond 0.18309 ( 82) hydrogen bonds : angle 9.80673 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.209 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: A 29 THR cc_start: 0.8988 (p) cc_final: 0.8675 (t) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2628 time to fit residues: 15.2270 Evaluate side-chains 34 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 42 HIS A 57 GLN A 160 GLN A 275 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.041108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.033613 restraints weight = 78927.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.035362 restraints weight = 37639.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.036540 restraints weight = 22184.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.037417 restraints weight = 14668.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.038053 restraints weight = 10472.179| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4022 Z= 0.179 Angle : 0.634 4.949 5479 Z= 0.350 Chirality : 0.044 0.147 607 Planarity : 0.004 0.037 720 Dihedral : 5.437 16.347 545 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.69 % Allowed : 3.21 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.38), residues: 502 helix: -0.67 (0.93), residues: 26 sheet: -0.23 (0.56), residues: 67 loop : 1.33 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 517 TYR 0.007 0.002 TYR A 301 PHE 0.021 0.002 PHE A 258 TRP 0.012 0.001 TRP A 205 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4004) covalent geometry : angle 0.63109 ( 5443) SS BOND : bond 0.00242 ( 18) SS BOND : angle 0.96114 ( 36) hydrogen bonds : bond 0.04798 ( 82) hydrogen bonds : angle 7.70231 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.202 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 370 ILE cc_start: 0.9663 (mt) cc_final: 0.9112 (tp) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.1584 time to fit residues: 7.5129 Evaluate side-chains 28 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 57 GLN A 302 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.040602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.033094 restraints weight = 80017.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.034817 restraints weight = 38477.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.035956 restraints weight = 22778.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036830 restraints weight = 15108.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.037468 restraints weight = 10792.947| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4022 Z= 0.160 Angle : 0.574 4.663 5479 Z= 0.309 Chirality : 0.042 0.145 607 Planarity : 0.004 0.063 720 Dihedral : 5.126 18.966 545 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.69 % Allowed : 4.82 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.38), residues: 502 helix: -0.42 (1.00), residues: 26 sheet: -0.73 (0.55), residues: 69 loop : 1.08 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 434 TYR 0.007 0.001 TYR A 112 PHE 0.013 0.001 PHE A 258 TRP 0.007 0.001 TRP A 205 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4004) covalent geometry : angle 0.57301 ( 5443) SS BOND : bond 0.00182 ( 18) SS BOND : angle 0.75643 ( 36) hydrogen bonds : bond 0.03885 ( 82) hydrogen bonds : angle 7.09770 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.160 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 370 ILE cc_start: 0.9723 (mt) cc_final: 0.9229 (tp) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.1634 time to fit residues: 5.7868 Evaluate side-chains 24 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.040070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032853 restraints weight = 83872.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.034534 restraints weight = 40175.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035627 restraints weight = 24015.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.036458 restraints weight = 15915.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.037102 restraints weight = 11363.634| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4022 Z= 0.159 Angle : 0.546 4.676 5479 Z= 0.291 Chirality : 0.041 0.142 607 Planarity : 0.004 0.043 720 Dihedral : 4.893 16.069 545 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.23 % Allowed : 5.73 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.38), residues: 502 helix: -0.49 (0.99), residues: 26 sheet: -0.80 (0.56), residues: 69 loop : 0.91 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 517 TYR 0.008 0.001 TYR A 112 PHE 0.012 0.001 PHE A 258 TRP 0.005 0.001 TRP A 205 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4004) covalent geometry : angle 0.54490 ( 5443) SS BOND : bond 0.00184 ( 18) SS BOND : angle 0.67010 ( 36) hydrogen bonds : bond 0.03383 ( 82) hydrogen bonds : angle 6.82418 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.219 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 370 ILE cc_start: 0.9703 (mt) cc_final: 0.9269 (tp) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.1483 time to fit residues: 4.5306 Evaluate side-chains 24 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.040049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.032821 restraints weight = 83393.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034526 restraints weight = 40096.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035622 restraints weight = 23747.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036450 restraints weight = 15766.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.037074 restraints weight = 11309.839| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4022 Z= 0.116 Angle : 0.512 4.513 5479 Z= 0.270 Chirality : 0.041 0.146 607 Planarity : 0.003 0.031 720 Dihedral : 4.697 15.578 545 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.23 % Allowed : 5.50 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.39), residues: 502 helix: -0.38 (0.99), residues: 26 sheet: -0.79 (0.67), residues: 57 loop : 0.83 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.007 0.001 TYR A 83 PHE 0.010 0.001 PHE A 258 TRP 0.005 0.001 TRP A 205 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4004) covalent geometry : angle 0.51094 ( 5443) SS BOND : bond 0.00163 ( 18) SS BOND : angle 0.60691 ( 36) hydrogen bonds : bond 0.03081 ( 82) hydrogen bonds : angle 6.57573 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.161 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: A 45 MET cc_start: 0.9684 (tmm) cc_final: 0.9447 (tmm) REVERT: A 275 ASN cc_start: 0.9440 (OUTLIER) cc_final: 0.9081 (m110) REVERT: A 370 ILE cc_start: 0.9708 (mt) cc_final: 0.9304 (tp) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1435 time to fit residues: 4.4937 Evaluate side-chains 21 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.039700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.032537 restraints weight = 85314.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.034155 restraints weight = 41034.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035269 restraints weight = 24681.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.036093 restraints weight = 16301.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036701 restraints weight = 11631.650| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4022 Z= 0.143 Angle : 0.528 4.533 5479 Z= 0.277 Chirality : 0.041 0.138 607 Planarity : 0.003 0.030 720 Dihedral : 4.617 16.614 545 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.46 % Allowed : 6.42 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.38), residues: 502 helix: -0.52 (0.98), residues: 26 sheet: -0.94 (0.68), residues: 57 loop : 0.74 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.008 0.001 TYR A 83 PHE 0.010 0.001 PHE A 258 TRP 0.005 0.001 TRP A 169 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4004) covalent geometry : angle 0.52675 ( 5443) SS BOND : bond 0.00191 ( 18) SS BOND : angle 0.63363 ( 36) hydrogen bonds : bond 0.03024 ( 82) hydrogen bonds : angle 6.51926 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.217 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: A 370 ILE cc_start: 0.9752 (mt) cc_final: 0.9356 (tp) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.1190 time to fit residues: 3.4342 Evaluate side-chains 21 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 275 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.039545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.032485 restraints weight = 84739.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.034127 restraints weight = 40486.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035216 restraints weight = 23916.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036013 restraints weight = 15835.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.036610 restraints weight = 11298.910| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4022 Z= 0.130 Angle : 0.510 4.569 5479 Z= 0.267 Chirality : 0.041 0.143 607 Planarity : 0.003 0.030 720 Dihedral : 4.550 16.241 545 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.69 % Allowed : 6.65 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.39), residues: 502 helix: -0.51 (0.98), residues: 26 sheet: -0.94 (0.61), residues: 69 loop : 0.81 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.008 0.001 TYR A 83 PHE 0.009 0.001 PHE A 258 TRP 0.005 0.001 TRP A 169 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4004) covalent geometry : angle 0.50920 ( 5443) SS BOND : bond 0.00173 ( 18) SS BOND : angle 0.58568 ( 36) hydrogen bonds : bond 0.02818 ( 82) hydrogen bonds : angle 6.37699 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.199 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: A 275 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.8894 (m110) REVERT: A 370 ILE cc_start: 0.9754 (mt) cc_final: 0.9352 (tp) outliers start: 3 outliers final: 0 residues processed: 21 average time/residue: 0.0802 time to fit residues: 2.4565 Evaluate side-chains 20 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3146 r_free = 0.3146 target = 0.039728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.032539 restraints weight = 83555.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.034213 restraints weight = 39849.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.035329 restraints weight = 23506.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.036135 restraints weight = 15618.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.036739 restraints weight = 11242.036| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4022 Z= 0.089 Angle : 0.485 4.389 5479 Z= 0.252 Chirality : 0.042 0.147 607 Planarity : 0.003 0.030 720 Dihedral : 4.383 15.816 545 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.23 % Allowed : 7.11 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.39), residues: 502 helix: -0.32 (1.00), residues: 26 sheet: -1.09 (0.68), residues: 57 loop : 0.86 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.008 0.001 TYR A 83 PHE 0.008 0.001 PHE A 258 TRP 0.005 0.001 TRP A 205 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 4004) covalent geometry : angle 0.48438 ( 5443) SS BOND : bond 0.00157 ( 18) SS BOND : angle 0.54414 ( 36) hydrogen bonds : bond 0.02745 ( 82) hydrogen bonds : angle 6.19592 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.228 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: A 275 ASN cc_start: 0.9350 (OUTLIER) cc_final: 0.8873 (m110) REVERT: A 282 MET cc_start: 0.9498 (mtm) cc_final: 0.8837 (mtm) REVERT: A 370 ILE cc_start: 0.9748 (mt) cc_final: 0.9348 (tp) REVERT: A 488 ASN cc_start: 0.9274 (t0) cc_final: 0.9048 (t0) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1044 time to fit residues: 3.0410 Evaluate side-chains 21 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.0000 chunk 26 optimal weight: 0.0020 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.040001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032595 restraints weight = 81435.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.034293 restraints weight = 39401.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035424 restraints weight = 23411.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036255 restraints weight = 15602.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036877 restraints weight = 11197.110| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4022 Z= 0.078 Angle : 0.463 4.176 5479 Z= 0.238 Chirality : 0.042 0.145 607 Planarity : 0.003 0.030 720 Dihedral : 4.118 16.630 545 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.23 % Allowed : 7.11 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.40), residues: 502 helix: -0.19 (1.01), residues: 26 sheet: -1.22 (0.65), residues: 57 loop : 1.02 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 517 TYR 0.008 0.001 TYR A 83 PHE 0.009 0.001 PHE A 258 TRP 0.007 0.001 TRP A 205 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 4004) covalent geometry : angle 0.46271 ( 5443) SS BOND : bond 0.00161 ( 18) SS BOND : angle 0.55370 ( 36) hydrogen bonds : bond 0.02336 ( 82) hydrogen bonds : angle 5.89357 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.223 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 275 ASN cc_start: 0.9362 (OUTLIER) cc_final: 0.9156 (m110) REVERT: A 370 ILE cc_start: 0.9742 (mt) cc_final: 0.9383 (tp) REVERT: A 488 ASN cc_start: 0.9304 (t0) cc_final: 0.9094 (t0) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.1081 time to fit residues: 3.2451 Evaluate side-chains 20 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3153 r_free = 0.3153 target = 0.039960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032615 restraints weight = 81240.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034293 restraints weight = 39261.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035408 restraints weight = 23227.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036243 restraints weight = 15468.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036854 restraints weight = 11102.378| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4022 Z= 0.083 Angle : 0.469 5.470 5479 Z= 0.240 Chirality : 0.041 0.144 607 Planarity : 0.003 0.029 720 Dihedral : 4.144 17.185 545 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.23 % Allowed : 7.34 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.40), residues: 502 helix: -0.31 (0.99), residues: 26 sheet: -1.27 (0.65), residues: 57 loop : 1.05 (0.34), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 517 TYR 0.008 0.001 TYR A 83 PHE 0.009 0.001 PHE A 258 TRP 0.005 0.001 TRP A 205 HIS 0.004 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 4004) covalent geometry : angle 0.46909 ( 5443) SS BOND : bond 0.00160 ( 18) SS BOND : angle 0.52097 ( 36) hydrogen bonds : bond 0.02265 ( 82) hydrogen bonds : angle 5.81460 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1004 Ramachandran restraints generated. 502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.207 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 347 MET cc_start: 0.9652 (mmm) cc_final: 0.9408 (mmm) REVERT: A 370 ILE cc_start: 0.9751 (mt) cc_final: 0.9395 (tp) REVERT: A 488 ASN cc_start: 0.9275 (t0) cc_final: 0.9061 (t0) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1328 time to fit residues: 3.5444 Evaluate side-chains 19 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.039659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.032420 restraints weight = 82243.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.034061 restraints weight = 39825.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035161 restraints weight = 23652.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.035969 restraints weight = 15741.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.036590 restraints weight = 11332.868| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4022 Z= 0.096 Angle : 0.469 4.560 5479 Z= 0.242 Chirality : 0.041 0.143 607 Planarity : 0.003 0.029 720 Dihedral : 4.130 16.365 545 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.23 % Allowed : 7.34 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.40), residues: 502 helix: -0.36 (0.99), residues: 26 sheet: -1.12 (0.73), residues: 47 loop : 0.98 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.008 0.001 TYR A 83 PHE 0.008 0.001 PHE A 258 TRP 0.005 0.001 TRP A 205 HIS 0.002 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 4004) covalent geometry : angle 0.46853 ( 5443) SS BOND : bond 0.00168 ( 18) SS BOND : angle 0.51530 ( 36) hydrogen bonds : bond 0.02281 ( 82) hydrogen bonds : angle 5.77331 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.21 seconds wall clock time: 29 minutes 45.46 seconds (1785.46 seconds total)