Starting phenix.real_space_refine on Tue Mar 3 17:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dc2_27320/03_2026/8dc2_27320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dc2_27320/03_2026/8dc2_27320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dc2_27320/03_2026/8dc2_27320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dc2_27320/03_2026/8dc2_27320.map" model { file = "/net/cci-nas-00/data/ceres_data/8dc2_27320/03_2026/8dc2_27320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dc2_27320/03_2026/8dc2_27320.cif" } resolution = 2.99 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= 0.179 sd= 1.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 132 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 32 5.16 5 C 4326 2.51 5 N 1221 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7296 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5483 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 10, 'TRANS': 662} Chain breaks: 2 Chain: "B" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1069 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 25} Link IDs: {'rna2p': 8, 'rna3p': 42} Chain: "C" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 542 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 1.65, per 1000 atoms: 0.23 Number of scatterers: 7296 At special positions: 0 Unit cell: (80.28, 92.545, 110.385, 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 32 16.00 P 86 15.00 O 1631 8.00 N 1221 7.00 C 4326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.63 Conformation dependent library (CDL) restraints added in 159.4 milliseconds 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1286 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 57.1% alpha, 10.5% beta 33 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 27 through 52 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.607A pdb=" N THR A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 132 through 146 Processing helix chain 'A' and resid 162 through 177 removed outlier: 4.302A pdb=" N ASN A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 199 through 215 removed outlier: 4.049A pdb=" N ARG A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 removed outlier: 3.944A pdb=" N LYS A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.707A pdb=" N LYS A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 413 through 435 removed outlier: 3.530A pdb=" N LYS A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 472 removed outlier: 3.882A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 483 through 486 Processing helix chain 'A' and resid 487 through 523 removed outlier: 3.501A pdb=" N GLY A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 611 removed outlier: 3.639A pdb=" N ILE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 4.280A pdb=" N ASN A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.786A pdb=" N VAL A 668 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 669 " --> pdb=" O HIS A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.842A pdb=" N MET A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.567A pdb=" N LYS A 733 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 250 removed outlier: 5.878A pdb=" N ASN A 317 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 302 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP A 315 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 304 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR A 313 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 306 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU A 311 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 312 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 391 removed outlier: 5.267A pdb=" N ILE A 348 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE A 391 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR A 346 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 334 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N LEU A 349 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 13.098A pdb=" N VAL A 332 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 333 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU A 530 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ILE A 335 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 527 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 634 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 529 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR A 718 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 720 " --> pdb=" O LEU A 633 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1697 1.33 - 1.45: 2004 1.45 - 1.57: 3690 1.57 - 1.69: 170 1.69 - 1.81: 56 Bond restraints: 7617 Sorted by residual: bond pdb=" CB GLU A 417 " pdb=" CG GLU A 417 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.99e+00 bond pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" N SER A 158 " pdb=" CA SER A 158 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.71e+00 bond pdb=" CG GLU A 417 " pdb=" CD GLU A 417 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" CA SER A 158 " pdb=" CB SER A 158 " ideal model delta sigma weight residual 1.530 1.510 0.020 1.69e-02 3.50e+03 1.36e+00 ... (remaining 7612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 10198 1.18 - 2.36: 375 2.36 - 3.54: 63 3.54 - 4.72: 16 4.72 - 5.90: 5 Bond angle restraints: 10657 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DA D -7 " ideal model delta sigma weight residual 120.20 123.90 -3.70 1.50e+00 4.44e-01 6.09e+00 angle pdb=" O3' U B -12 " pdb=" C3' U B -12 " pdb=" C2' U B -12 " ideal model delta sigma weight residual 113.70 117.04 -3.34 1.50e+00 4.44e-01 4.96e+00 angle pdb=" C3' U B -12 " pdb=" O3' U B -12 " pdb=" P G B -11 " ideal model delta sigma weight residual 120.20 123.48 -3.28 1.50e+00 4.44e-01 4.77e+00 angle pdb=" C SER A 158 " pdb=" CA SER A 158 " pdb=" CB SER A 158 " ideal model delta sigma weight residual 110.42 114.73 -4.31 1.99e+00 2.53e-01 4.69e+00 angle pdb=" C ASN A 338 " pdb=" CA ASN A 338 " pdb=" CB ASN A 338 " ideal model delta sigma weight residual 109.70 113.52 -3.82 1.81e+00 3.05e-01 4.45e+00 ... (remaining 10652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 4223 34.63 - 69.26: 289 69.26 - 103.89: 19 103.89 - 138.52: 1 138.52 - 173.15: 3 Dihedral angle restraints: 4535 sinusoidal: 2538 harmonic: 1997 Sorted by residual: dihedral pdb=" O4' U B 1 " pdb=" C1' U B 1 " pdb=" N1 U B 1 " pdb=" C2 U B 1 " ideal model delta sinusoidal sigma weight residual 232.00 58.85 173.15 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA MET A 607 " pdb=" C MET A 607 " pdb=" N ILE A 608 " pdb=" CA ILE A 608 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE A 157 " pdb=" C ILE A 157 " pdb=" N SER A 158 " pdb=" CA SER A 158 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 856 0.034 - 0.069: 268 0.069 - 0.103: 65 0.103 - 0.138: 24 0.138 - 0.172: 1 Chirality restraints: 1214 Sorted by residual: chirality pdb=" C3' U B -12 " pdb=" C4' U B -12 " pdb=" O3' U B -12 " pdb=" C2' U B -12 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CB THR A 165 " pdb=" CA THR A 165 " pdb=" OG1 THR A 165 " pdb=" CG2 THR A 165 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1211 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C -15 " 0.014 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" N9 DG C -15 " -0.011 2.00e-02 2.50e+03 pdb=" C8 DG C -15 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG C -15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG C -15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG C -15 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG C -15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG C -15 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C -15 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG C -15 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DG C -15 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG C -15 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 126 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C THR A 126 " -0.028 2.00e-02 2.50e+03 pdb=" O THR A 126 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 127 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B -3 " -0.019 2.00e-02 2.50e+03 1.07e-02 2.57e+00 pdb=" N1 C B -3 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C B -3 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C B -3 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C B -3 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C B -3 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C B -3 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C B -3 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C B -3 " 0.003 2.00e-02 2.50e+03 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 979 2.75 - 3.29: 7349 3.29 - 3.83: 13416 3.83 - 4.36: 15837 4.36 - 4.90: 24413 Nonbonded interactions: 61994 Sorted by model distance: nonbonded pdb=" OH TYR A 42 " pdb=" OD1 ASN A 140 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS A 155 " pdb=" O SER A 158 " model vdw 2.217 3.120 nonbonded pdb=" NE2 HIS A 612 " pdb=" OP1 DT C -8 " model vdw 2.289 3.120 nonbonded pdb=" O LEU A 121 " pdb=" ND2 ASN A 274 " model vdw 2.292 3.120 nonbonded pdb=" O2' U B -19 " pdb=" OP1 U B -16 " model vdw 2.301 3.040 ... (remaining 61989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:8.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7617 Z= 0.142 Angle : 0.544 5.898 10657 Z= 0.305 Chirality : 0.037 0.172 1214 Planarity : 0.003 0.029 1042 Dihedral : 19.786 173.155 3249 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % 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: 1.17 (0.33), residues: 667 helix: 1.96 (0.30), residues: 327 sheet: 0.43 (0.60), residues: 71 loop : -0.60 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.017 0.001 TYR A 133 PHE 0.017 0.001 PHE A 400 TRP 0.006 0.001 TRP A 429 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7617) covalent geometry : angle 0.54363 (10657) hydrogen bonds : bond 0.14088 ( 376) hydrogen bonds : angle 5.55034 ( 1000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.225 Fit side-chains REVERT: A 90 MET cc_start: 0.7248 (mtm) cc_final: 0.6849 (mtm) REVERT: A 174 MET cc_start: 0.6426 (mmp) cc_final: 0.6132 (mmt) REVERT: A 230 ASP cc_start: 0.7729 (t0) cc_final: 0.7518 (t0) REVERT: A 288 ASP cc_start: 0.7563 (t70) cc_final: 0.7332 (t70) REVERT: A 488 ASP cc_start: 0.8276 (p0) cc_final: 0.7965 (p0) REVERT: A 695 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7545 (t0) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.4362 time to fit residues: 62.2822 Evaluate side-chains 104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 140 ASN A 176 HIS A 265 ASN A 413 ASN A 605 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.075661 restraints weight = 15786.222| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.88 r_work: 0.3005 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7617 Z= 0.263 Angle : 0.628 6.773 10657 Z= 0.346 Chirality : 0.042 0.230 1214 Planarity : 0.004 0.032 1042 Dihedral : 21.900 171.982 1889 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.93 % Allowed : 11.76 % Favored : 86.31 % 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: 1.01 (0.33), residues: 667 helix: 1.68 (0.29), residues: 335 sheet: 0.19 (0.59), residues: 71 loop : -0.47 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 240 TYR 0.022 0.002 TYR A 133 PHE 0.015 0.002 PHE A 613 TRP 0.019 0.003 TRP A 185 HIS 0.006 0.002 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 7617) covalent geometry : angle 0.62847 (10657) hydrogen bonds : bond 0.05075 ( 376) hydrogen bonds : angle 4.59991 ( 1000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8631 (tp30) cc_final: 0.8315 (tp30) REVERT: A 230 ASP cc_start: 0.8497 (t0) cc_final: 0.8072 (t0) REVERT: A 233 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8086 (pp) REVERT: A 288 ASP cc_start: 0.8590 (t70) cc_final: 0.8353 (t70) REVERT: A 363 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: A 488 ASP cc_start: 0.8565 (p0) cc_final: 0.7977 (p0) outliers start: 12 outliers final: 4 residues processed: 113 average time/residue: 0.4366 time to fit residues: 52.5526 Evaluate side-chains 104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 ASN ** 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 = 0.3378 r_free = 0.3378 target = 0.090537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077531 restraints weight = 15643.253| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.89 r_work: 0.3043 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7617 Z= 0.176 Angle : 0.560 5.452 10657 Z= 0.311 Chirality : 0.038 0.200 1214 Planarity : 0.003 0.027 1042 Dihedral : 21.771 172.405 1887 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.90 % Allowed : 13.69 % Favored : 83.41 % 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: 1.02 (0.33), residues: 667 helix: 1.66 (0.29), residues: 335 sheet: 0.17 (0.59), residues: 71 loop : -0.42 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 240 TYR 0.019 0.002 TYR A 133 PHE 0.012 0.001 PHE A 613 TRP 0.010 0.002 TRP A 185 HIS 0.002 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7617) covalent geometry : angle 0.55995 (10657) hydrogen bonds : bond 0.04428 ( 376) hydrogen bonds : angle 4.33338 ( 1000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8563 (tp30) cc_final: 0.8144 (tp30) REVERT: A 148 MET cc_start: 0.8007 (tpt) cc_final: 0.7627 (tpp) REVERT: A 206 MET cc_start: 0.8140 (mmm) cc_final: 0.7607 (mmt) REVERT: A 230 ASP cc_start: 0.8502 (t0) cc_final: 0.8075 (t0) REVERT: A 233 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.7955 (pp) REVERT: A 288 ASP cc_start: 0.8553 (t70) cc_final: 0.8307 (t70) REVERT: A 340 LYS cc_start: 0.8818 (tppp) cc_final: 0.8607 (tppp) REVERT: A 363 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: A 488 ASP cc_start: 0.8521 (p0) cc_final: 0.7974 (p0) REVERT: A 642 MET cc_start: 0.8419 (ttp) cc_final: 0.7990 (tpp) REVERT: A 695 ASN cc_start: 0.8103 (t0) cc_final: 0.7445 (t0) outliers start: 18 outliers final: 4 residues processed: 118 average time/residue: 0.4308 time to fit residues: 54.3713 Evaluate side-chains 112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 347 ASN A 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.075333 restraints weight = 16010.676| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.91 r_work: 0.2999 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7617 Z= 0.249 Angle : 0.601 5.097 10657 Z= 0.334 Chirality : 0.041 0.227 1214 Planarity : 0.003 0.028 1042 Dihedral : 21.882 170.461 1887 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.38 % Allowed : 15.30 % Favored : 81.32 % 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: 0.86 (0.33), residues: 667 helix: 1.48 (0.29), residues: 346 sheet: 0.06 (0.58), residues: 69 loop : -0.50 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 699 TYR 0.022 0.002 TYR A 133 PHE 0.013 0.002 PHE A 604 TRP 0.011 0.002 TRP A 179 HIS 0.004 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 7617) covalent geometry : angle 0.60065 (10657) hydrogen bonds : bond 0.04803 ( 376) hydrogen bonds : angle 4.48162 ( 1000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8662 (tp30) cc_final: 0.8229 (tp30) REVERT: A 206 MET cc_start: 0.8164 (mmm) cc_final: 0.7723 (mmt) REVERT: A 230 ASP cc_start: 0.8513 (t0) cc_final: 0.8117 (t0) REVERT: A 233 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8047 (pp) REVERT: A 288 ASP cc_start: 0.8622 (t70) cc_final: 0.8365 (t70) REVERT: A 337 VAL cc_start: 0.8863 (t) cc_final: 0.8585 (p) REVERT: A 488 ASP cc_start: 0.8522 (p0) cc_final: 0.7963 (p0) REVERT: A 695 ASN cc_start: 0.8078 (t0) cc_final: 0.7413 (t0) outliers start: 21 outliers final: 8 residues processed: 113 average time/residue: 0.4357 time to fit residues: 52.6328 Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 522 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.080119 restraints weight = 15920.782| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.90 r_work: 0.3089 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7617 Z= 0.125 Angle : 0.520 5.197 10657 Z= 0.292 Chirality : 0.037 0.170 1214 Planarity : 0.003 0.028 1042 Dihedral : 21.663 173.616 1887 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.42 % Allowed : 17.55 % Favored : 80.03 % 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: 1.11 (0.33), residues: 667 helix: 1.71 (0.29), residues: 348 sheet: 0.09 (0.59), residues: 69 loop : -0.41 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.014 0.001 TYR A 133 PHE 0.009 0.001 PHE A 396 TRP 0.008 0.001 TRP A 179 HIS 0.002 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7617) covalent geometry : angle 0.52018 (10657) hydrogen bonds : bond 0.04057 ( 376) hydrogen bonds : angle 4.17756 ( 1000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.228 Fit side-chains REVERT: A 59 GLU cc_start: 0.8528 (tp30) cc_final: 0.8057 (tp30) REVERT: A 206 MET cc_start: 0.8148 (mmm) cc_final: 0.7658 (mmt) REVERT: A 230 ASP cc_start: 0.8436 (t0) cc_final: 0.8031 (t0) REVERT: A 233 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8000 (pp) REVERT: A 288 ASP cc_start: 0.8589 (t70) cc_final: 0.8316 (t70) REVERT: A 488 ASP cc_start: 0.8445 (p0) cc_final: 0.7924 (p0) REVERT: A 499 ASN cc_start: 0.8474 (t0) cc_final: 0.8097 (t0) REVERT: A 642 MET cc_start: 0.8470 (ttp) cc_final: 0.8104 (tpp) REVERT: A 695 ASN cc_start: 0.8062 (t0) cc_final: 0.7423 (t0) outliers start: 15 outliers final: 6 residues processed: 121 average time/residue: 0.4401 time to fit residues: 56.7739 Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 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 169 GLN A 347 ASN A 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.089935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076941 restraints weight = 15817.405| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.90 r_work: 0.3030 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7617 Z= 0.203 Angle : 0.586 6.993 10657 Z= 0.322 Chirality : 0.040 0.206 1214 Planarity : 0.003 0.028 1042 Dihedral : 21.759 172.599 1887 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.90 % Allowed : 18.04 % Favored : 79.07 % 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: 1.00 (0.33), residues: 667 helix: 1.58 (0.29), residues: 350 sheet: 0.06 (0.60), residues: 69 loop : -0.41 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 240 TYR 0.022 0.002 TYR A 133 PHE 0.017 0.002 PHE A 400 TRP 0.045 0.004 TRP A 185 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 7617) covalent geometry : angle 0.58589 (10657) hydrogen bonds : bond 0.04464 ( 376) hydrogen bonds : angle 4.26804 ( 1000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8620 (tp30) cc_final: 0.8116 (tp30) REVERT: A 167 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8268 (tmm) REVERT: A 169 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7725 (tp40) REVERT: A 175 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8104 (tm-30) REVERT: A 206 MET cc_start: 0.8156 (mmm) cc_final: 0.7702 (mmt) REVERT: A 230 ASP cc_start: 0.8496 (t0) cc_final: 0.8096 (t0) REVERT: A 233 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8029 (pp) REVERT: A 288 ASP cc_start: 0.8637 (t70) cc_final: 0.8374 (t70) REVERT: A 399 LEU cc_start: 0.8677 (mt) cc_final: 0.8429 (mp) REVERT: A 488 ASP cc_start: 0.8479 (p0) cc_final: 0.7960 (p0) REVERT: A 695 ASN cc_start: 0.8029 (t0) cc_final: 0.7372 (t0) outliers start: 18 outliers final: 8 residues processed: 109 average time/residue: 0.4489 time to fit residues: 52.0894 Evaluate side-chains 109 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 347 ASN A 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074602 restraints weight = 16019.266| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.90 r_work: 0.2983 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7617 Z= 0.285 Angle : 0.672 11.161 10657 Z= 0.364 Chirality : 0.043 0.238 1214 Planarity : 0.004 0.030 1042 Dihedral : 21.940 169.555 1887 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.06 % Allowed : 19.00 % Favored : 77.94 % 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: 0.72 (0.33), residues: 667 helix: 1.32 (0.28), residues: 352 sheet: -0.02 (0.61), residues: 69 loop : -0.53 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 240 TYR 0.023 0.002 TYR A 133 PHE 0.021 0.002 PHE A 396 TRP 0.034 0.004 TRP A 185 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 7617) covalent geometry : angle 0.67187 (10657) hydrogen bonds : bond 0.04978 ( 376) hydrogen bonds : angle 4.48279 ( 1000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8688 (tp30) cc_final: 0.8177 (tp30) REVERT: A 169 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: A 175 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 206 MET cc_start: 0.8159 (mmm) cc_final: 0.7724 (mmt) REVERT: A 230 ASP cc_start: 0.8521 (t0) cc_final: 0.8196 (t0) REVERT: A 288 ASP cc_start: 0.8685 (t70) cc_final: 0.8411 (t70) REVERT: A 488 ASP cc_start: 0.8517 (p0) cc_final: 0.7962 (p0) REVERT: A 695 ASN cc_start: 0.7956 (t0) cc_final: 0.7383 (t0) outliers start: 19 outliers final: 9 residues processed: 107 average time/residue: 0.4372 time to fit residues: 49.9198 Evaluate side-chains 105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 169 GLN A 347 ASN A 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.089806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.076764 restraints weight = 16075.641| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.92 r_work: 0.3024 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7617 Z= 0.194 Angle : 0.619 9.475 10657 Z= 0.336 Chirality : 0.041 0.222 1214 Planarity : 0.003 0.028 1042 Dihedral : 21.823 171.609 1887 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.74 % Allowed : 20.45 % Favored : 76.81 % 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: 0.80 (0.33), residues: 667 helix: 1.37 (0.29), residues: 346 sheet: -0.01 (0.61), residues: 69 loop : -0.40 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.019 0.002 TYR A 133 PHE 0.015 0.002 PHE A 400 TRP 0.027 0.003 TRP A 185 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7617) covalent geometry : angle 0.61940 (10657) hydrogen bonds : bond 0.04448 ( 376) hydrogen bonds : angle 4.38787 ( 1000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8628 (tp30) cc_final: 0.8126 (tp30) REVERT: A 175 GLU cc_start: 0.8490 (tm-30) cc_final: 0.7939 (tm-30) REVERT: A 206 MET cc_start: 0.8171 (mmm) cc_final: 0.7704 (mmt) REVERT: A 230 ASP cc_start: 0.8494 (t0) cc_final: 0.8191 (t0) REVERT: A 288 ASP cc_start: 0.8666 (t70) cc_final: 0.8399 (t70) REVERT: A 488 ASP cc_start: 0.8481 (p0) cc_final: 0.7943 (p0) REVERT: A 607 MET cc_start: 0.8386 (ptm) cc_final: 0.8079 (ppp) REVERT: A 693 MET cc_start: 0.8911 (mmm) cc_final: 0.8702 (mmm) REVERT: A 695 ASN cc_start: 0.7943 (t0) cc_final: 0.7370 (t0) outliers start: 17 outliers final: 6 residues processed: 115 average time/residue: 0.4149 time to fit residues: 51.1915 Evaluate side-chains 104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 0.3980 chunk 42 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 347 ASN A 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079361 restraints weight = 15794.101| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.89 r_work: 0.3076 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7617 Z= 0.143 Angle : 0.597 8.966 10657 Z= 0.323 Chirality : 0.039 0.192 1214 Planarity : 0.003 0.027 1042 Dihedral : 21.717 173.520 1887 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.58 % Allowed : 21.90 % Favored : 75.52 % 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: 0.86 (0.34), residues: 667 helix: 1.44 (0.29), residues: 344 sheet: -0.06 (0.58), residues: 69 loop : -0.37 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.016 0.001 TYR A 133 PHE 0.016 0.001 PHE A 396 TRP 0.025 0.002 TRP A 185 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7617) covalent geometry : angle 0.59729 (10657) hydrogen bonds : bond 0.04210 ( 376) hydrogen bonds : angle 4.28223 ( 1000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8566 (tp30) cc_final: 0.8053 (tp30) REVERT: A 175 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 206 MET cc_start: 0.8169 (mmm) cc_final: 0.7671 (mmt) REVERT: A 230 ASP cc_start: 0.8497 (t0) cc_final: 0.8037 (t0) REVERT: A 234 LYS cc_start: 0.8679 (mppt) cc_final: 0.8463 (mppt) REVERT: A 288 ASP cc_start: 0.8621 (t70) cc_final: 0.8354 (t70) REVERT: A 444 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8009 (mp0) REVERT: A 488 ASP cc_start: 0.8419 (p0) cc_final: 0.7909 (p0) REVERT: A 499 ASN cc_start: 0.8464 (t0) cc_final: 0.8027 (t0) REVERT: A 695 ASN cc_start: 0.7913 (t0) cc_final: 0.7347 (t0) outliers start: 16 outliers final: 8 residues processed: 114 average time/residue: 0.4209 time to fit residues: 51.3577 Evaluate side-chains 110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077088 restraints weight = 15994.886| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.90 r_work: 0.3034 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7617 Z= 0.209 Angle : 0.653 10.795 10657 Z= 0.351 Chirality : 0.041 0.291 1214 Planarity : 0.003 0.028 1042 Dihedral : 21.774 172.794 1887 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.61 % Allowed : 23.51 % Favored : 74.88 % 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: 0.77 (0.33), residues: 667 helix: 1.39 (0.29), residues: 344 sheet: -0.05 (0.58), residues: 69 loop : -0.47 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 699 TYR 0.020 0.002 TYR A 133 PHE 0.018 0.002 PHE A 400 TRP 0.028 0.003 TRP A 185 HIS 0.002 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 7617) covalent geometry : angle 0.65302 (10657) hydrogen bonds : bond 0.04508 ( 376) hydrogen bonds : angle 4.37563 ( 1000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8627 (tp30) cc_final: 0.8104 (tp30) REVERT: A 175 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 206 MET cc_start: 0.8167 (mmm) cc_final: 0.7674 (mmt) REVERT: A 230 ASP cc_start: 0.8461 (t0) cc_final: 0.8019 (t0) REVERT: A 288 ASP cc_start: 0.8642 (t70) cc_final: 0.8374 (t70) REVERT: A 488 ASP cc_start: 0.8465 (p0) cc_final: 0.7948 (p0) REVERT: A 695 ASN cc_start: 0.7939 (t0) cc_final: 0.7398 (t0) outliers start: 10 outliers final: 7 residues processed: 110 average time/residue: 0.4328 time to fit residues: 50.8523 Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.079657 restraints weight = 15843.273| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.89 r_work: 0.3086 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7617 Z= 0.152 Angle : 0.618 9.813 10657 Z= 0.334 Chirality : 0.039 0.219 1214 Planarity : 0.003 0.027 1042 Dihedral : 21.695 174.132 1887 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.45 % Allowed : 23.67 % Favored : 74.88 % 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: 0.90 (0.34), residues: 667 helix: 1.52 (0.29), residues: 344 sheet: -0.06 (0.57), residues: 69 loop : -0.41 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 130 TYR 0.016 0.001 TYR A 133 PHE 0.018 0.001 PHE A 212 TRP 0.023 0.002 TRP A 185 HIS 0.002 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7617) covalent geometry : angle 0.61809 (10657) hydrogen bonds : bond 0.04273 ( 376) hydrogen bonds : angle 4.29046 ( 1000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2166.78 seconds wall clock time: 37 minutes 49.81 seconds (2269.81 seconds total)