Starting phenix.real_space_refine on Wed Jun 3 14:34:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vc6_64944/06_2026/9vc6_64944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vc6_64944/06_2026/9vc6_64944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vc6_64944/06_2026/9vc6_64944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vc6_64944/06_2026/9vc6_64944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vc6_64944/06_2026/9vc6_64944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vc6_64944/06_2026/9vc6_64944.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 Zn 1 6.06 5 S 18 5.16 5 C 4162 2.51 5 N 1006 2.21 5 O 1159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6346 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6138 Classifications: {'peptide': 775} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 745} Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 208 Unusual residues: {' ZN': 1, 'AV0': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.52, per 1000 atoms: 0.24 Number of scatterers: 6346 At special positions: 0 Unit cell: (83, 78.5733, 110.667, 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) Zn 1 29.99 S 18 16.00 O 1159 8.00 N 1006 7.00 C 4162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 175 " distance=2.09 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: 0.43 Conformation dependent library (CDL) restraints added in 443.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" NE2 HIS A 700 " pdb="ZN ZN A 804 " - pdb=" NE2 HIS A 582 " 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 60.0% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid -1 through 23 Processing helix chain 'A' and resid 25 through 41 Processing helix chain 'A' and resid 45 through 71 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 181 through 201 Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 239 through 258 Processing helix chain 'A' and resid 261 through 273 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 329 through 345 removed outlier: 3.825A pdb=" N LEU A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.846A pdb=" N LEU A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 380 Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 393 through 415 Proline residue: A 403 - end of helix Processing helix chain 'A' and resid 419 through 441 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 454 through 474 Processing helix chain 'A' and resid 476 through 497 removed outlier: 3.866A pdb=" N ALA A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 585 through 593 removed outlier: 3.961A pdb=" N SER A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 621 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 698 through 702 Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 750 through 754 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 93 removed outlier: 7.950A pdb=" N LYS A 108 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP A 164 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 114 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 170 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 169 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL A 136 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N SER A 171 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N SER A 134 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N TRP A 173 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N PHE A 132 " --> pdb=" O TRP A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 383 Processing sheet with id=AA3, first strand: chain 'A' and resid 624 through 628 removed outlier: 9.997A pdb=" N SER A 624 " --> pdb=" O LYS A 594 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP A 596 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 626 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 598 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL A 628 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR A 600 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A 572 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 598 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 574 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR A 600 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 527 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE A 574 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N MET A 529 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 633 through 636 removed outlier: 6.269A pdb=" N VAL A 659 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG A 668 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LYS A 696 " --> pdb=" O ARG A 668 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 670 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU A 695 " --> pdb=" O LEU A 720 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1062 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: 1.12 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1393 1.33 - 1.46: 2143 1.46 - 1.59: 2926 1.59 - 1.72: 0 1.72 - 1.85: 31 Bond restraints: 6493 Sorted by residual: bond pdb=" CE1 HIS A 243 " pdb=" NE2 HIS A 243 " ideal model delta sigma weight residual 1.321 1.365 -0.044 1.00e-02 1.00e+04 1.98e+01 bond pdb=" CA SER A 134 " pdb=" CB SER A 134 " ideal model delta sigma weight residual 1.530 1.462 0.068 1.55e-02 4.16e+03 1.94e+01 bond pdb=" CE1 HIS A 378 " pdb=" NE2 HIS A 378 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.65e+01 bond pdb=" CA SER A 645 " pdb=" CB SER A 645 " ideal model delta sigma weight residual 1.536 1.483 0.053 1.50e-02 4.44e+03 1.23e+01 bond pdb=" CE1 HIS A 604 " pdb=" NE2 HIS A 604 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 8.84e+00 ... (remaining 6488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 6985 1.58 - 3.17: 1604 3.17 - 4.75: 213 4.75 - 6.34: 26 6.34 - 7.92: 2 Bond angle restraints: 8830 Sorted by residual: angle pdb=" CA SER A 645 " pdb=" C SER A 645 " pdb=" N PRO A 646 " ideal model delta sigma weight residual 118.33 122.91 -4.58 1.00e+00 1.00e+00 2.09e+01 angle pdb=" CA PHE A 135 " pdb=" CB PHE A 135 " pdb=" CG PHE A 135 " ideal model delta sigma weight residual 113.80 118.26 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CA PHE A 407 " pdb=" CB PHE A 407 " pdb=" CG PHE A 407 " ideal model delta sigma weight residual 113.80 109.38 4.42 1.00e+00 1.00e+00 1.96e+01 angle pdb=" O SER A 645 " pdb=" C SER A 645 " pdb=" N PRO A 646 " ideal model delta sigma weight residual 121.83 118.54 3.29 7.80e-01 1.64e+00 1.78e+01 angle pdb=" N VAL A 511 " pdb=" CA VAL A 511 " pdb=" C VAL A 511 " ideal model delta sigma weight residual 112.43 108.76 3.67 9.20e-01 1.18e+00 1.59e+01 ... (remaining 8825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 3819 25.86 - 51.71: 211 51.71 - 77.57: 36 77.57 - 103.43: 3 103.43 - 129.28: 7 Dihedral angle restraints: 4076 sinusoidal: 1837 harmonic: 2239 Sorted by residual: dihedral pdb=" CBQ AV0 A 801 " pdb=" CBT AV0 A 801 " pdb=" CCM AV0 A 801 " pdb=" OBV AV0 A 801 " ideal model delta sinusoidal sigma weight residual 306.95 177.67 129.28 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" CBQ AV0 A 803 " pdb=" CBT AV0 A 803 " pdb=" CCM AV0 A 803 " pdb=" OBV AV0 A 803 " ideal model delta sinusoidal sigma weight residual -53.05 -170.69 117.64 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" CA GLN A 150 " pdb=" C GLN A 150 " pdb=" N PHE A 151 " pdb=" CA PHE A 151 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 599 0.056 - 0.111: 340 0.111 - 0.167: 96 0.167 - 0.222: 23 0.222 - 0.278: 3 Chirality restraints: 1061 Sorted by residual: chirality pdb=" CB VAL A 65 " pdb=" CA VAL A 65 " pdb=" CG1 VAL A 65 " pdb=" CG2 VAL A 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL A 718 " pdb=" CA VAL A 718 " pdb=" CG1 VAL A 718 " pdb=" CG2 VAL A 718 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL A 486 " pdb=" CA VAL A 486 " pdb=" CG1 VAL A 486 " pdb=" CG2 VAL A 486 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1058 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 164 " -0.057 2.00e-02 2.50e+03 2.77e-02 1.92e+01 pdb=" CG TRP A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 164 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 164 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 164 " -0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 164 " 0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 164 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 600 " 0.057 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR A 600 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 600 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 600 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 600 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 600 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 600 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 600 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 407 " 0.038 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE A 407 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 407 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 407 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 407 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 407 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 407 " 0.013 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 12 2.51 - 3.11: 4468 3.11 - 3.71: 9305 3.71 - 4.30: 14256 4.30 - 4.90: 23269 Nonbonded interactions: 51310 Sorted by model distance: nonbonded pdb=" OD2 ASP A 674 " pdb="ZN ZN A 804 " model vdw 1.916 2.230 nonbonded pdb=" OE1 GLU A 68 " pdb=" OH TYR A 325 " model vdw 2.228 3.040 nonbonded pdb=" O GLY A 724 " pdb=" ND2 ASN A 727 " model vdw 2.343 3.120 nonbonded pdb=" O GLY A 673 " pdb=" NZ LYS A 696 " model vdw 2.351 3.120 nonbonded pdb=" O ALA A 238 " pdb=" OG1 THR A 338 " model vdw 2.424 3.040 ... (remaining 51305 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: 1.300 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.320 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 : 0.010 0.242 6496 Z= 0.612 Angle : 1.330 7.919 8832 Z= 0.870 Chirality : 0.072 0.278 1061 Planarity : 0.008 0.042 1070 Dihedral : 16.556 129.283 2633 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.80 % Allowed : 9.90 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.26), residues: 773 helix: -0.55 (0.22), residues: 417 sheet: 0.68 (0.45), residues: 107 loop : -0.99 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 161 TYR 0.057 0.009 TYR A 600 PHE 0.049 0.008 PHE A 407 TRP 0.057 0.010 TRP A 164 HIS 0.012 0.004 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00953 / 0.60 ( 6493) covalent geometry : angle 1.32753 / 0.87 ( 8830) SS BOND : bond 0.06355 / 3.97 ( 1) SS BOND : angle 5.24578 / 2.03 ( 2) hydrogen bonds : bond 0.15765 / 9.98 ( 375) hydrogen bonds : angle 6.29279 / 4.43 ( 1062) metal coordination : bond 0.17094 / 9.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.256 Fit side-chains REVERT: A 80 GLN cc_start: 0.7839 (mt0) cc_final: 0.6948 (mm-40) REVERT: A 91 GLU cc_start: 0.7276 (tp30) cc_final: 0.7075 (tm-30) REVERT: A 202 SER cc_start: 0.6872 (m) cc_final: 0.6638 (p) REVERT: A 223 GLU cc_start: 0.6950 (tt0) cc_final: 0.5931 (mp0) REVERT: A 389 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5432 (tp) REVERT: A 474 ARG cc_start: 0.6253 (mtt180) cc_final: 0.5730 (mtt-85) REVERT: A 489 PHE cc_start: 0.7155 (m-10) cc_final: 0.6885 (m-10) REVERT: A 493 TRP cc_start: 0.7541 (t60) cc_final: 0.7321 (t-100) REVERT: A 508 MET cc_start: 0.9320 (ttp) cc_final: 0.9083 (ttp) REVERT: A 609 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6353 (mm-30) REVERT: A 652 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6473 (mm-30) REVERT: A 768 ARG cc_start: 0.8667 (ttm-80) cc_final: 0.7584 (ttp80) outliers start: 12 outliers final: 3 residues processed: 102 average time/residue: 0.5289 time to fit residues: 56.7521 Evaluate side-chains 85 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 609 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 178 GLN A 435 GLN A 577 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117345 restraints weight = 6810.433| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.63 r_work: 0.3165 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6496 Z= 0.141 Angle : 0.545 6.689 8832 Z= 0.277 Chirality : 0.041 0.148 1061 Planarity : 0.004 0.044 1070 Dihedral : 10.430 139.559 1224 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.55 % Allowed : 12.29 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.04 (0.29), residues: 773 helix: 1.21 (0.25), residues: 422 sheet: 0.95 (0.49), residues: 102 loop : -0.18 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 154 TYR 0.009 0.001 TYR A 198 PHE 0.017 0.001 PHE A 407 TRP 0.013 0.002 TRP A 164 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6493) covalent geometry : angle 0.54485 / 0.28 ( 8830) SS BOND : bond 0.00281 / 0.18 ( 1) SS BOND : angle 1.06746 / 0.45 ( 2) hydrogen bonds : bond 0.04563 / 3.06 ( 375) hydrogen bonds : angle 4.64501 / 3.29 ( 1062) metal coordination : bond 0.00075 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.248 Fit side-chains REVERT: A 80 GLN cc_start: 0.8361 (mt0) cc_final: 0.7999 (mp10) REVERT: A 223 GLU cc_start: 0.7777 (tt0) cc_final: 0.7067 (mp0) REVERT: A 229 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: A 474 ARG cc_start: 0.7127 (mtt180) cc_final: 0.6744 (mtt-85) REVERT: A 489 PHE cc_start: 0.7813 (m-10) cc_final: 0.7431 (m-10) REVERT: A 493 TRP cc_start: 0.8205 (t60) cc_final: 0.7968 (t-100) REVERT: A 652 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 768 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.7922 (ttp80) outliers start: 17 outliers final: 6 residues processed: 94 average time/residue: 0.5771 time to fit residues: 56.8391 Evaluate side-chains 85 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 685 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.147529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120356 restraints weight = 6774.301| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.52 r_work: 0.3106 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6496 Z= 0.131 Angle : 0.517 7.999 8832 Z= 0.259 Chirality : 0.041 0.149 1061 Planarity : 0.004 0.044 1070 Dihedral : 9.397 139.519 1217 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.70 % Allowed : 13.64 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.55 (0.30), residues: 773 helix: 1.76 (0.25), residues: 421 sheet: 0.87 (0.49), residues: 102 loop : -0.07 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.008 0.001 TYR A 325 PHE 0.016 0.001 PHE A 407 TRP 0.011 0.001 TRP A 164 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6493) covalent geometry : angle 0.51665 / 0.26 ( 8830) SS BOND : bond 0.00108 / 0.07 ( 1) SS BOND : angle 0.89757 / 0.39 ( 2) hydrogen bonds : bond 0.04182 / 2.83 ( 375) hydrogen bonds : angle 4.44202 / 3.15 ( 1062) metal coordination : bond 0.00243 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.181 Fit side-chains REVERT: A 80 GLN cc_start: 0.8387 (mt0) cc_final: 0.8041 (mp10) REVERT: A 223 GLU cc_start: 0.7804 (tt0) cc_final: 0.7103 (mp0) REVERT: A 229 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: A 474 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6740 (mtt-85) REVERT: A 489 PHE cc_start: 0.7824 (m-10) cc_final: 0.7351 (m-10) REVERT: A 493 TRP cc_start: 0.8343 (t60) cc_final: 0.8141 (t-100) REVERT: A 652 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 686 PHE cc_start: 0.7363 (m-80) cc_final: 0.6892 (m-80) REVERT: A 744 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: A 768 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.7928 (ttp80) outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 0.5513 time to fit residues: 55.0464 Evaluate side-chains 90 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 744 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119568 restraints weight = 6743.163| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.55 r_work: 0.3001 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6496 Z= 0.128 Angle : 0.511 8.174 8832 Z= 0.256 Chirality : 0.041 0.154 1061 Planarity : 0.004 0.041 1070 Dihedral : 9.205 142.015 1217 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.45 % Allowed : 14.09 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.73 (0.30), residues: 773 helix: 1.95 (0.25), residues: 421 sheet: 0.86 (0.50), residues: 95 loop : -0.03 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 548 TYR 0.007 0.001 TYR A 743 PHE 0.013 0.001 PHE A 183 TRP 0.009 0.001 TRP A 469 HIS 0.002 0.001 HIS A 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6493) covalent geometry : angle 0.50960 / 0.26 ( 8830) SS BOND : bond 0.00258 / 0.16 ( 1) SS BOND : angle 2.42923 / 0.92 ( 2) hydrogen bonds : bond 0.04035 / 2.73 ( 375) hydrogen bonds : angle 4.35022 / 3.08 ( 1062) metal coordination : bond 0.00233 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.235 Fit side-chains REVERT: A 80 GLN cc_start: 0.8400 (mt0) cc_final: 0.7984 (mp10) REVERT: A 89 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8086 (t70) REVERT: A 223 GLU cc_start: 0.7721 (tt0) cc_final: 0.6934 (mp0) REVERT: A 229 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: A 474 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6739 (mtt-85) REVERT: A 489 PHE cc_start: 0.7791 (m-10) cc_final: 0.7363 (m-10) REVERT: A 493 TRP cc_start: 0.8320 (t60) cc_final: 0.8092 (t-100) REVERT: A 652 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 686 PHE cc_start: 0.7345 (m-80) cc_final: 0.6899 (m-80) REVERT: A 708 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7283 (t70) REVERT: A 733 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7778 (t0) REVERT: A 768 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.7905 (ttp80) outliers start: 23 outliers final: 12 residues processed: 98 average time/residue: 0.4946 time to fit residues: 51.1618 Evaluate side-chains 94 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 733 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120837 restraints weight = 6834.943| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.56 r_work: 0.3141 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6496 Z= 0.111 Angle : 0.495 9.327 8832 Z= 0.247 Chirality : 0.040 0.181 1061 Planarity : 0.004 0.041 1070 Dihedral : 9.016 143.282 1217 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.55 % Allowed : 14.69 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.80 (0.30), residues: 773 helix: 2.13 (0.25), residues: 421 sheet: 0.44 (0.51), residues: 92 loop : -0.03 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 262 TYR 0.006 0.001 TYR A 198 PHE 0.012 0.001 PHE A 183 TRP 0.009 0.001 TRP A 469 HIS 0.002 0.000 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6493) covalent geometry : angle 0.48964 / 0.25 ( 8830) SS BOND : bond 0.01887 / 1.18 ( 1) SS BOND : angle 4.73458 / 1.79 ( 2) hydrogen bonds : bond 0.03565 / 2.41 ( 375) hydrogen bonds : angle 4.23309 / 3.00 ( 1062) metal coordination : bond 0.00202 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.242 Fit side-chains REVERT: A 80 GLN cc_start: 0.8416 (mt0) cc_final: 0.8071 (mp10) REVERT: A 89 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7949 (t70) REVERT: A 223 GLU cc_start: 0.7763 (tt0) cc_final: 0.7088 (mp0) REVERT: A 229 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: A 474 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6778 (mtt-85) REVERT: A 489 PHE cc_start: 0.7784 (m-10) cc_final: 0.7346 (m-10) REVERT: A 493 TRP cc_start: 0.8363 (t60) cc_final: 0.8063 (t-100) REVERT: A 652 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 686 PHE cc_start: 0.7311 (m-80) cc_final: 0.6931 (m-80) REVERT: A 733 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7721 (t0) REVERT: A 768 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.7949 (ttp80) outliers start: 17 outliers final: 8 residues processed: 91 average time/residue: 0.5502 time to fit residues: 52.6682 Evaluate side-chains 87 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 733 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.0030 chunk 28 optimal weight: 0.0270 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.5650 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.149349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.121230 restraints weight = 6806.036| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.56 r_work: 0.3145 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6496 Z= 0.107 Angle : 0.485 7.920 8832 Z= 0.243 Chirality : 0.040 0.157 1061 Planarity : 0.004 0.039 1070 Dihedral : 8.959 144.490 1217 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.75 % Allowed : 13.64 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.88 (0.30), residues: 773 helix: 2.21 (0.25), residues: 421 sheet: 0.43 (0.51), residues: 92 loop : 0.00 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.006 0.001 TYR A 325 PHE 0.012 0.001 PHE A 183 TRP 0.008 0.001 TRP A 469 HIS 0.002 0.000 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6493) covalent geometry : angle 0.48231 / 0.24 ( 8830) SS BOND : bond 0.01264 / 0.79 ( 1) SS BOND : angle 3.43160 / 1.27 ( 2) hydrogen bonds : bond 0.03522 / 2.39 ( 375) hydrogen bonds : angle 4.20155 / 2.98 ( 1062) metal coordination : bond 0.00134 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.248 Fit side-chains REVERT: A 80 GLN cc_start: 0.8407 (mt0) cc_final: 0.8065 (mp10) REVERT: A 89 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7909 (t70) REVERT: A 138 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: A 223 GLU cc_start: 0.7743 (tt0) cc_final: 0.7073 (mp0) REVERT: A 229 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: A 474 ARG cc_start: 0.7225 (mtt180) cc_final: 0.6826 (mtt-85) REVERT: A 489 PHE cc_start: 0.7732 (m-10) cc_final: 0.7293 (m-10) REVERT: A 493 TRP cc_start: 0.8305 (t60) cc_final: 0.8060 (t-100) REVERT: A 547 ARG cc_start: 0.7470 (mpt-90) cc_final: 0.7216 (mpt-90) REVERT: A 652 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 686 PHE cc_start: 0.7278 (m-80) cc_final: 0.6940 (m-80) REVERT: A 733 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7765 (t0) REVERT: A 744 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: A 768 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.7948 (ttp80) outliers start: 25 outliers final: 10 residues processed: 93 average time/residue: 0.5578 time to fit residues: 54.5924 Evaluate side-chains 91 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 744 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.148300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121281 restraints weight = 6802.113| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.51 r_work: 0.3103 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6496 Z= 0.120 Angle : 0.503 8.256 8832 Z= 0.252 Chirality : 0.041 0.163 1061 Planarity : 0.004 0.038 1070 Dihedral : 9.033 145.286 1217 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.45 % Allowed : 14.09 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.83 (0.30), residues: 773 helix: 2.28 (0.25), residues: 415 sheet: 0.13 (0.49), residues: 102 loop : -0.06 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.007 0.001 TYR A 499 PHE 0.012 0.001 PHE A 183 TRP 0.008 0.001 TRP A 469 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6493) covalent geometry : angle 0.50110 / 0.25 ( 8830) SS BOND : bond 0.01114 / 0.70 ( 1) SS BOND : angle 3.07545 / 1.17 ( 2) hydrogen bonds : bond 0.03762 / 2.55 ( 375) hydrogen bonds : angle 4.20164 / 2.99 ( 1062) metal coordination : bond 0.00218 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.179 Fit side-chains REVERT: A 80 GLN cc_start: 0.8450 (mt0) cc_final: 0.8071 (mp10) REVERT: A 138 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: A 223 GLU cc_start: 0.7745 (tt0) cc_final: 0.7046 (mp0) REVERT: A 229 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: A 474 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6817 (mtt-85) REVERT: A 489 PHE cc_start: 0.7724 (m-10) cc_final: 0.7282 (m-10) REVERT: A 493 TRP cc_start: 0.8273 (t60) cc_final: 0.8047 (t-100) REVERT: A 547 ARG cc_start: 0.7408 (mpt-90) cc_final: 0.7077 (mpt-90) REVERT: A 652 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 686 PHE cc_start: 0.7329 (m-80) cc_final: 0.7010 (m-80) REVERT: A 708 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7190 (t70) REVERT: A 733 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7767 (t0) REVERT: A 744 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6409 (mp0) REVERT: A 768 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.7945 (ttp80) outliers start: 23 outliers final: 13 residues processed: 92 average time/residue: 0.5093 time to fit residues: 49.5257 Evaluate side-chains 95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 744 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.147662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120231 restraints weight = 6759.693| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.55 r_work: 0.3093 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6496 Z= 0.138 Angle : 0.534 8.658 8832 Z= 0.265 Chirality : 0.041 0.179 1061 Planarity : 0.004 0.039 1070 Dihedral : 9.203 146.482 1217 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.85 % Allowed : 14.84 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.72 (0.30), residues: 773 helix: 2.18 (0.25), residues: 415 sheet: 0.13 (0.49), residues: 102 loop : -0.11 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.008 0.001 TYR A 499 PHE 0.013 0.001 PHE A 183 TRP 0.008 0.001 TRP A 469 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6493) covalent geometry : angle 0.53069 / 0.26 ( 8830) SS BOND : bond 0.01452 / 0.91 ( 1) SS BOND : angle 3.77510 / 1.38 ( 2) hydrogen bonds : bond 0.04058 / 2.75 ( 375) hydrogen bonds : angle 4.29161 / 3.05 ( 1062) metal coordination : bond 0.00252 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.225 Fit side-chains REVERT: A 80 GLN cc_start: 0.8506 (mt0) cc_final: 0.8056 (mp10) REVERT: A 138 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: A 223 GLU cc_start: 0.7768 (tt0) cc_final: 0.7078 (mp0) REVERT: A 229 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: A 474 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6796 (mtt-85) REVERT: A 489 PHE cc_start: 0.7787 (m-10) cc_final: 0.7355 (m-10) REVERT: A 547 ARG cc_start: 0.7407 (mpt-90) cc_final: 0.7069 (mpt-90) REVERT: A 652 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 686 PHE cc_start: 0.7352 (m-80) cc_final: 0.7030 (m-80) REVERT: A 708 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7207 (t70) REVERT: A 733 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7760 (t0) REVERT: A 744 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: A 768 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.7932 (ttp80) outliers start: 19 outliers final: 11 residues processed: 88 average time/residue: 0.5030 time to fit residues: 46.6825 Evaluate side-chains 92 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 744 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.147887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119386 restraints weight = 6928.250| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.62 r_work: 0.3199 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6496 Z= 0.104 Angle : 0.495 9.257 8832 Z= 0.244 Chirality : 0.040 0.165 1061 Planarity : 0.004 0.037 1070 Dihedral : 9.078 146.877 1217 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.70 % Allowed : 15.14 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.81 (0.30), residues: 773 helix: 2.30 (0.25), residues: 415 sheet: 0.13 (0.49), residues: 102 loop : -0.12 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.005 0.001 TYR A 743 PHE 0.016 0.001 PHE A 407 TRP 0.008 0.001 TRP A 469 HIS 0.002 0.000 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 6493) covalent geometry : angle 0.49283 / 0.24 ( 8830) SS BOND : bond 0.01148 / 0.72 ( 1) SS BOND : angle 3.04246 / 1.10 ( 2) hydrogen bonds : bond 0.03442 / 2.33 ( 375) hydrogen bonds : angle 4.15582 / 2.96 ( 1062) metal coordination : bond 0.00144 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.240 Fit side-chains REVERT: A 80 GLN cc_start: 0.8430 (mt0) cc_final: 0.8048 (mp10) REVERT: A 223 GLU cc_start: 0.7716 (tt0) cc_final: 0.7026 (mp0) REVERT: A 229 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: A 474 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6763 (mtt-85) REVERT: A 489 PHE cc_start: 0.7696 (m-10) cc_final: 0.7250 (m-10) REVERT: A 503 GLU cc_start: 0.8314 (pt0) cc_final: 0.8065 (pt0) REVERT: A 547 ARG cc_start: 0.7403 (mpt-90) cc_final: 0.7091 (mpt-90) REVERT: A 652 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 708 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7206 (t70) REVERT: A 733 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7740 (t0) REVERT: A 744 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: A 768 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.7899 (ttp80) outliers start: 18 outliers final: 10 residues processed: 88 average time/residue: 0.5858 time to fit residues: 54.1711 Evaluate side-chains 89 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 744 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.148219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120241 restraints weight = 6722.525| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.53 r_work: 0.3114 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6496 Z= 0.127 Angle : 0.535 12.664 8832 Z= 0.262 Chirality : 0.041 0.185 1061 Planarity : 0.004 0.038 1070 Dihedral : 9.214 147.114 1217 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.40 % Allowed : 15.89 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.75 (0.30), residues: 773 helix: 2.23 (0.25), residues: 415 sheet: 0.09 (0.49), residues: 102 loop : -0.13 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.007 0.001 TYR A 499 PHE 0.015 0.001 PHE A 407 TRP 0.008 0.001 TRP A 469 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6493) covalent geometry : angle 0.53328 / 0.26 ( 8830) SS BOND : bond 0.01222 / 0.76 ( 1) SS BOND : angle 3.24991 / 1.19 ( 2) hydrogen bonds : bond 0.03860 / 2.62 ( 375) hydrogen bonds : angle 4.26080 / 3.03 ( 1062) metal coordination : bond 0.00219 / 0.12 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.182 Fit side-chains REVERT: A 80 GLN cc_start: 0.8484 (mt0) cc_final: 0.8054 (mp10) REVERT: A 223 GLU cc_start: 0.7756 (tt0) cc_final: 0.7074 (mp0) REVERT: A 229 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: A 474 ARG cc_start: 0.7182 (mtt180) cc_final: 0.6783 (mtt-85) REVERT: A 489 PHE cc_start: 0.7770 (m-10) cc_final: 0.7336 (m-10) REVERT: A 503 GLU cc_start: 0.8316 (pt0) cc_final: 0.8073 (pt0) REVERT: A 547 ARG cc_start: 0.7396 (mpt-90) cc_final: 0.7067 (mpt-90) REVERT: A 652 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7373 (mm-30) REVERT: A 686 PHE cc_start: 0.7352 (m-80) cc_final: 0.7032 (m-80) REVERT: A 708 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7239 (t70) REVERT: A 733 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7760 (t0) REVERT: A 744 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6409 (mp0) REVERT: A 768 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.7931 (ttp80) outliers start: 16 outliers final: 11 residues processed: 87 average time/residue: 0.5496 time to fit residues: 50.3292 Evaluate side-chains 90 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 744 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 25 optimal weight: 0.0870 chunk 26 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.148161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119730 restraints weight = 6889.284| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.62 r_work: 0.3195 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6496 Z= 0.102 Angle : 0.506 12.992 8832 Z= 0.246 Chirality : 0.040 0.171 1061 Planarity : 0.004 0.037 1070 Dihedral : 9.120 148.241 1217 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.70 % Allowed : 15.74 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.85 (0.30), residues: 773 helix: 2.34 (0.25), residues: 415 sheet: 0.11 (0.49), residues: 102 loop : -0.11 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.006 0.001 TYR A 198 PHE 0.012 0.001 PHE A 459 TRP 0.008 0.001 TRP A 544 HIS 0.002 0.000 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 6493) covalent geometry : angle 0.50481 / 0.24 ( 8830) SS BOND : bond 0.01069 / 0.67 ( 1) SS BOND : angle 2.76442 / 1.01 ( 2) hydrogen bonds : bond 0.03392 / 2.30 ( 375) hydrogen bonds : angle 4.16053 / 2.96 ( 1062) metal coordination : bond 0.00167 / 0.09 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2335.29 seconds wall clock time: 40 minutes 30.65 seconds (2430.65 seconds total)