Starting phenix.real_space_refine on Thu Jul 2 12:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lis_63122/07_2026/9lis_63122.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lis_63122/07_2026/9lis_63122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lis_63122/07_2026/9lis_63122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lis_63122/07_2026/9lis_63122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lis_63122/07_2026/9lis_63122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lis_63122/07_2026/9lis_63122.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 220 5.49 5 Mg 3 5.21 5 S 27 5.16 5 C 4598 2.51 5 N 1611 2.21 5 O 2197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3984 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 473} Chain: "B" Number of atoms: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 4061 Classifications: {'RNA': 190} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 13, 'rna3p_pur': 86, 'rna3p_pyr': 73} Link IDs: {'rna2p': 31, 'rna3p': 158} Chain: "C" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 257 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1878 SG CYS A 234 14.790 13.267 59.977 1.00184.78 S ATOM 1903 SG CYS A 237 12.169 10.493 59.449 1.00191.88 S ATOM 2131 SG CYS A 265 15.574 10.279 57.759 1.00180.06 S Time building chain proxies: 2.17, per 1000 atoms: 0.25 Number of scatterers: 8657 At special positions: 0 Unit cell: (96.744, 107.586, 120.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 220 15.00 Mg 3 11.99 O 2197 8.00 N 1611 7.00 C 4598 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: 0.82 Conformation dependent library (CDL) restraints added in 180.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 268 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 237 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 265 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 234 " Number of angles added : 3 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 5 sheets defined 36.8% alpha, 11.1% beta 65 base pairs and 123 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 4.076A pdb=" N ILE A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 88 through 121 removed outlier: 4.304A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N CYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 183 Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.618A pdb=" N MET A 201 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 275 through 294 Processing helix chain 'A' and resid 298 through 314 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 322 through 334 Processing helix chain 'A' and resid 341 through 351 removed outlier: 4.232A pdb=" N CYS A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 461 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 5.919A pdb=" N TYR A 5 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU A 44 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A 7 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 41 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.443A pdb=" N LEU A 57 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLU A 192 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 59 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 396 removed outlier: 4.509A pdb=" N ALA A 395 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 386 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 476 through 478 removed outlier: 3.535A pdb=" N TYR A 477 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A 455 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER A 443 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 446 " --> pdb=" O GLN A 483 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 168 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 123 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1638 1.33 - 1.45: 3289 1.45 - 1.57: 3882 1.57 - 1.69: 437 1.69 - 1.81: 42 Bond restraints: 9288 Sorted by residual: bond pdb=" C3' DA C 36 " pdb=" C2' DA C 36 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT C 26 " pdb=" C2' DT C 26 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.58e+00 bond pdb=" C3' DA C 32 " pdb=" C2' DA C 32 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.38e+00 bond pdb=" C3' DC C 30 " pdb=" C2' DC C 30 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.27e+00 bond pdb=" C3' DG D 16 " pdb=" O3' DG D 16 " ideal model delta sigma weight residual 1.435 1.406 0.029 1.30e-02 5.92e+03 5.11e+00 ... (remaining 9283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 13082 1.68 - 3.35: 409 3.35 - 5.03: 67 5.03 - 6.71: 20 6.71 - 8.39: 6 Bond angle restraints: 13584 Sorted by residual: angle pdb=" C1' U B 171 " pdb=" N1 U B 171 " pdb=" C2 U B 171 " ideal model delta sigma weight residual 117.70 125.01 -7.31 1.20e+00 6.94e-01 3.71e+01 angle pdb=" O2 U B 93 " pdb=" C2 U B 93 " pdb=" N3 U B 93 " ideal model delta sigma weight residual 122.20 118.21 3.99 7.00e-01 2.04e+00 3.25e+01 angle pdb=" N1 U B 93 " pdb=" C2 U B 93 " pdb=" O2 U B 93 " ideal model delta sigma weight residual 122.80 126.79 -3.99 7.00e-01 2.04e+00 3.25e+01 angle pdb=" O2 C B 46 " pdb=" C2 C B 46 " pdb=" N3 C B 46 " ideal model delta sigma weight residual 121.90 118.07 3.83 7.00e-01 2.04e+00 2.99e+01 angle pdb=" N1 C B 46 " pdb=" C2 C B 46 " pdb=" O2 C B 46 " ideal model delta sigma weight residual 118.90 122.08 -3.18 6.00e-01 2.78e+00 2.81e+01 ... (remaining 13579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 5049 35.98 - 71.95: 630 71.95 - 107.93: 71 107.93 - 143.91: 3 143.91 - 179.89: 6 Dihedral angle restraints: 5759 sinusoidal: 4321 harmonic: 1438 Sorted by residual: dihedral pdb=" O4' C B 46 " pdb=" C1' C B 46 " pdb=" N1 C B 46 " pdb=" C2 C B 46 " ideal model delta sinusoidal sigma weight residual -160.00 -25.89 -134.11 1 1.50e+01 4.44e-03 7.24e+01 dihedral pdb=" O4' C B 80 " pdb=" C1' C B 80 " pdb=" N1 C B 80 " pdb=" C2 C B 80 " ideal model delta sinusoidal sigma weight residual 232.00 52.11 179.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 94 " pdb=" C1' U B 94 " pdb=" N1 U B 94 " pdb=" C2 U B 94 " ideal model delta sinusoidal sigma weight residual 232.00 58.63 173.37 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 5756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1379 0.047 - 0.095: 227 0.095 - 0.142: 33 0.142 - 0.189: 6 0.189 - 0.236: 4 Chirality restraints: 1649 Sorted by residual: chirality pdb=" C1' A B 70 " pdb=" O4' A B 70 " pdb=" C2' A B 70 " pdb=" N9 A B 70 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C3' U B 191 " pdb=" C4' U B 191 " pdb=" O3' U B 191 " pdb=" C2' U B 191 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3' A B 83 " pdb=" C4' A B 83 " pdb=" O3' A B 83 " pdb=" C2' A B 83 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1646 not shown) Planarity restraints: 927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 163 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO A 164 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 71 " -0.031 2.00e-02 2.50e+03 1.46e-02 5.85e+00 pdb=" N9 A B 71 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A B 71 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 71 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 71 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B 71 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 71 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 71 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 71 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B 71 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 71 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 70 " -0.029 2.00e-02 2.50e+03 1.36e-02 5.08e+00 pdb=" N9 A B 70 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A B 70 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B 70 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 70 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 70 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B 70 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 70 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 70 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 70 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 70 " 0.002 2.00e-02 2.50e+03 ... (remaining 924 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 112 2.63 - 3.20: 7414 3.20 - 3.77: 17065 3.77 - 4.33: 21067 4.33 - 4.90: 29440 Nonbonded interactions: 75098 Sorted by model distance: nonbonded pdb=" ND1 HIS A 245 " pdb="MG MG A 603 " model vdw 2.064 2.250 nonbonded pdb=" N7 G B 48 " pdb="MG MG B 501 " model vdw 2.068 2.250 nonbonded pdb=" NE2 HIS A 269 " pdb="MG MG A 603 " model vdw 2.074 2.250 nonbonded pdb=" NE2 HIS A 273 " pdb="MG MG A 603 " model vdw 2.113 2.250 nonbonded pdb=" O2 U B 62 " pdb=" N2 G B 117 " model vdw 2.278 2.496 ... (remaining 75093 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: 1.100 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.690 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.004 0.048 9292 Z= 0.324 Angle : 0.726 8.385 13587 Z= 0.577 Chirality : 0.038 0.236 1649 Planarity : 0.005 0.069 927 Dihedral : 24.717 179.886 4835 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.34 % Favored : 89.25 % Rotamer: Outliers : 3.26 % Allowed : 31.93 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.48 (0.38), residues: 493 helix: 1.05 (0.40), residues: 161 sheet: -2.26 (0.60), residues: 68 loop : -2.00 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 213 TYR 0.026 0.001 TYR A 305 PHE 0.006 0.001 PHE A 198 TRP 0.005 0.001 TRP A 478 HIS 0.004 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.32 ( 9288) covalent geometry : angle 0.72608 / 0.58 (13584) hydrogen bonds : bond 0.13574 / 8.86 ( 313) hydrogen bonds : angle 6.14083 / 4.27 ( 701) metal coordination : bond 0.02047 / 1.02 ( 4) metal coordination : angle 1.27079 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ASN cc_start: 0.8794 (t0) cc_final: 0.8438 (t0) REVERT: A 213 ARG cc_start: 0.8871 (mtm-85) cc_final: 0.8526 (mtm-85) REVERT: A 356 LYS cc_start: 0.9270 (mmmm) cc_final: 0.8983 (mmmm) REVERT: A 402 MET cc_start: 0.7910 (mmm) cc_final: 0.7564 (mmm) REVERT: A 452 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9063 (pt) outliers start: 14 outliers final: 13 residues processed: 52 average time/residue: 0.0544 time to fit residues: 4.3010 Evaluate side-chains 55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.078996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056762 restraints weight = 32426.346| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.81 r_work: 0.2975 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.146 9292 Z= 0.406 Angle : 0.734 9.145 13587 Z= 0.419 Chirality : 0.046 0.236 1649 Planarity : 0.007 0.068 927 Dihedral : 25.220 179.469 3832 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.78 % Favored : 87.02 % Rotamer: Outliers : 7.46 % Allowed : 27.74 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.37), residues: 493 helix: 0.78 (0.40), residues: 162 sheet: -2.03 (0.60), residues: 66 loop : -2.38 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 486 TYR 0.021 0.002 TYR A 305 PHE 0.011 0.002 PHE A 124 TRP 0.005 0.001 TRP A 161 HIS 0.007 0.002 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.41 ( 9288) covalent geometry : angle 0.73202 / 0.42 (13584) hydrogen bonds : bond 0.08657 / 5.66 ( 313) hydrogen bonds : angle 4.88500 / 3.28 ( 701) metal coordination : bond 0.04052 / 2.02 ( 4) metal coordination : angle 3.59363 / 1.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 39 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8235 (mm) REVERT: A 356 LYS cc_start: 0.9318 (mmmm) cc_final: 0.8973 (mmmm) REVERT: A 402 MET cc_start: 0.7719 (mmm) cc_final: 0.7335 (mmm) REVERT: A 420 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8329 (t0) outliers start: 32 outliers final: 19 residues processed: 67 average time/residue: 0.0662 time to fit residues: 6.4752 Evaluate side-chains 59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 69 optimal weight: 50.0000 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.081689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.059519 restraints weight = 31535.179| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.52 r_work: 0.3054 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9292 Z= 0.159 Angle : 0.555 6.238 13587 Z= 0.327 Chirality : 0.035 0.234 1649 Planarity : 0.005 0.060 927 Dihedral : 25.223 179.269 3827 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.94 % Favored : 89.86 % Rotamer: Outliers : 6.29 % Allowed : 28.90 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.46 (0.39), residues: 493 helix: 1.21 (0.41), residues: 162 sheet: -2.04 (0.60), residues: 77 loop : -2.15 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 213 TYR 0.009 0.001 TYR A 305 PHE 0.008 0.001 PHE A 318 TRP 0.005 0.001 TRP A 478 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 9288) covalent geometry : angle 0.55453 / 0.33 (13584) hydrogen bonds : bond 0.06354 / 4.05 ( 313) hydrogen bonds : angle 4.33669 / 2.92 ( 701) metal coordination : bond 0.01839 / 0.92 ( 4) metal coordination : angle 1.75590 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8172 (ttmt) REVERT: A 193 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 203 ASN cc_start: 0.8782 (t0) cc_final: 0.8436 (t0) REVERT: A 210 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: A 356 LYS cc_start: 0.9287 (mmmm) cc_final: 0.8913 (mmmm) REVERT: A 420 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8221 (t0) outliers start: 27 outliers final: 19 residues processed: 66 average time/residue: 0.0805 time to fit residues: 7.4220 Evaluate side-chains 65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 50.0000 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 0.0040 chunk 44 optimal weight: 0.7980 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.081337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059281 restraints weight = 32153.067| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.53 r_work: 0.3041 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9292 Z= 0.185 Angle : 0.551 6.495 13587 Z= 0.324 Chirality : 0.036 0.243 1649 Planarity : 0.005 0.071 927 Dihedral : 25.140 179.746 3827 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.76 % Favored : 88.03 % Rotamer: Outliers : 7.23 % Allowed : 28.44 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.37 (0.39), residues: 493 helix: 1.31 (0.41), residues: 162 sheet: -1.92 (0.62), residues: 77 loop : -2.14 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.011 0.001 TYR A 305 PHE 0.007 0.001 PHE A 318 TRP 0.004 0.001 TRP A 478 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 ( 9288) covalent geometry : angle 0.55073 / 0.32 (13584) hydrogen bonds : bond 0.06441 / 4.15 ( 313) hydrogen bonds : angle 4.21154 / 2.83 ( 701) metal coordination : bond 0.02132 / 1.06 ( 4) metal coordination : angle 1.63371 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: A 193 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 203 ASN cc_start: 0.8795 (t0) cc_final: 0.8448 (t0) REVERT: A 210 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8713 (tm-30) REVERT: A 356 LYS cc_start: 0.9304 (mmmm) cc_final: 0.8927 (mmmm) REVERT: A 420 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8290 (t0) outliers start: 31 outliers final: 23 residues processed: 65 average time/residue: 0.0715 time to fit residues: 6.8059 Evaluate side-chains 70 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 40.0000 chunk 33 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 47 optimal weight: 0.0770 chunk 62 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 overall best weight: 3.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.079822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057710 restraints weight = 31981.824| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.56 r_work: 0.3019 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 9292 Z= 0.226 Angle : 0.572 6.103 13587 Z= 0.334 Chirality : 0.037 0.251 1649 Planarity : 0.005 0.061 927 Dihedral : 25.150 179.780 3827 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.56 % Favored : 88.24 % Rotamer: Outliers : 6.99 % Allowed : 28.67 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.49 (0.39), residues: 493 helix: 1.23 (0.41), residues: 162 sheet: -2.00 (0.61), residues: 77 loop : -2.22 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 480 TYR 0.015 0.002 TYR A 305 PHE 0.008 0.001 PHE A 453 TRP 0.004 0.001 TRP A 478 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.23 ( 9288) covalent geometry : angle 0.57092 / 0.33 (13584) hydrogen bonds : bond 0.06859 / 4.41 ( 313) hydrogen bonds : angle 4.20213 / 2.81 ( 701) metal coordination : bond 0.02388 / 1.19 ( 4) metal coordination : angle 2.21763 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8204 (ttmt) REVERT: A 193 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 203 ASN cc_start: 0.8849 (t0) cc_final: 0.8483 (t0) REVERT: A 210 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8616 (tm-30) REVERT: A 292 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8865 (tptp) REVERT: A 356 LYS cc_start: 0.9348 (mmmm) cc_final: 0.8998 (mmmm) REVERT: A 420 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8241 (t0) outliers start: 30 outliers final: 24 residues processed: 66 average time/residue: 0.0786 time to fit residues: 7.4990 Evaluate side-chains 72 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.079977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.058018 restraints weight = 31833.137| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.48 r_work: 0.3029 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 9292 Z= 0.215 Angle : 0.557 5.658 13587 Z= 0.327 Chirality : 0.037 0.285 1649 Planarity : 0.005 0.060 927 Dihedral : 25.182 179.692 3827 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.36 % Favored : 88.44 % Rotamer: Outliers : 7.46 % Allowed : 28.67 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.53 (0.39), residues: 493 helix: 1.22 (0.41), residues: 162 sheet: -2.09 (0.61), residues: 77 loop : -2.24 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.013 0.001 TYR A 305 PHE 0.007 0.001 PHE A 318 TRP 0.004 0.001 TRP A 478 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 ( 9288) covalent geometry : angle 0.55585 / 0.33 (13584) hydrogen bonds : bond 0.06717 / 4.30 ( 313) hydrogen bonds : angle 4.15936 / 2.78 ( 701) metal coordination : bond 0.02239 / 1.12 ( 4) metal coordination : angle 2.04030 / 1.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 47 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8173 (ttmt) REVERT: A 193 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8249 (mm) REVERT: A 203 ASN cc_start: 0.8827 (t0) cc_final: 0.8462 (t0) REVERT: A 210 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: A 292 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8872 (tptp) REVERT: A 356 LYS cc_start: 0.9356 (mmmm) cc_final: 0.8991 (mmmm) REVERT: A 420 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8285 (t0) outliers start: 32 outliers final: 22 residues processed: 72 average time/residue: 0.0630 time to fit residues: 6.5627 Evaluate side-chains 70 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 30.0000 chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.082796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060933 restraints weight = 31581.107| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.53 r_work: 0.3076 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9292 Z= 0.127 Angle : 0.526 8.798 13587 Z= 0.305 Chirality : 0.033 0.272 1649 Planarity : 0.004 0.060 927 Dihedral : 25.136 179.261 3827 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.94 % Favored : 89.86 % Rotamer: Outliers : 4.66 % Allowed : 31.24 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.44 (0.39), residues: 493 helix: 1.28 (0.42), residues: 168 sheet: -2.06 (0.70), residues: 55 loop : -2.30 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 113 TYR 0.006 0.001 TYR A 484 PHE 0.008 0.001 PHE A 318 TRP 0.005 0.001 TRP A 478 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 ( 9288) covalent geometry : angle 0.52589 / 0.31 (13584) hydrogen bonds : bond 0.05848 / 3.78 ( 313) hydrogen bonds : angle 3.97539 / 2.67 ( 701) metal coordination : bond 0.01471 / 0.73 ( 4) metal coordination : angle 1.23335 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 203 ASN cc_start: 0.8868 (t0) cc_final: 0.8548 (t0) REVERT: A 210 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: A 292 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8853 (tptp) REVERT: A 356 LYS cc_start: 0.9311 (mmmm) cc_final: 0.8898 (mmmm) outliers start: 20 outliers final: 14 residues processed: 62 average time/residue: 0.0837 time to fit residues: 7.3800 Evaluate side-chains 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.079894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057846 restraints weight = 31915.348| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.69 r_work: 0.2997 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 9292 Z= 0.295 Angle : 0.623 7.818 13587 Z= 0.353 Chirality : 0.040 0.280 1649 Planarity : 0.005 0.061 927 Dihedral : 25.152 179.595 3824 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.16 % Favored : 88.64 % Rotamer: Outliers : 5.83 % Allowed : 31.24 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.60 (0.38), residues: 493 helix: 1.27 (0.41), residues: 162 sheet: -2.13 (0.70), residues: 55 loop : -2.41 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 110 TYR 0.026 0.002 TYR A 305 PHE 0.017 0.002 PHE A 137 TRP 0.002 0.001 TRP A 478 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.29 ( 9288) covalent geometry : angle 0.62198 / 0.35 (13584) hydrogen bonds : bond 0.07272 / 4.69 ( 313) hydrogen bonds : angle 4.18340 / 2.78 ( 701) metal coordination : bond 0.02856 / 1.42 ( 4) metal coordination : angle 2.21016 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8196 (ttmt) REVERT: A 192 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 193 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8118 (mm) REVERT: A 203 ASN cc_start: 0.8930 (t0) cc_final: 0.8541 (t0) REVERT: A 210 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: A 292 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8924 (tptp) REVERT: A 356 LYS cc_start: 0.9370 (mmmm) cc_final: 0.9008 (mmmm) REVERT: A 420 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8476 (t0) outliers start: 25 outliers final: 17 residues processed: 64 average time/residue: 0.0698 time to fit residues: 6.5431 Evaluate side-chains 65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 66 optimal weight: 40.0000 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 40.0000 chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.082762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.060896 restraints weight = 31118.173| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.49 r_work: 0.3082 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9292 Z= 0.128 Angle : 0.545 9.119 13587 Z= 0.309 Chirality : 0.034 0.283 1649 Planarity : 0.004 0.059 927 Dihedral : 25.162 179.302 3824 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.75 % Favored : 89.05 % Rotamer: Outliers : 4.20 % Allowed : 32.63 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.38), residues: 493 helix: 1.27 (0.41), residues: 168 sheet: -2.16 (0.69), residues: 55 loop : -2.42 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 113 TYR 0.026 0.001 TYR A 305 PHE 0.009 0.001 PHE A 318 TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 ( 9288) covalent geometry : angle 0.54466 / 0.31 (13584) hydrogen bonds : bond 0.05921 / 3.80 ( 313) hydrogen bonds : angle 3.95283 / 2.64 ( 701) metal coordination : bond 0.01513 / 0.76 ( 4) metal coordination : angle 1.29894 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8266 (ttmt) REVERT: A 203 ASN cc_start: 0.8898 (t0) cc_final: 0.8544 (t0) REVERT: A 207 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8079 (tp-100) REVERT: A 210 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: A 292 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8868 (tptp) REVERT: A 356 LYS cc_start: 0.9287 (mmmm) cc_final: 0.8891 (mmmm) outliers start: 18 outliers final: 14 residues processed: 62 average time/residue: 0.0917 time to fit residues: 7.9886 Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.082365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059941 restraints weight = 32074.655| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.54 r_work: 0.3057 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9292 Z= 0.158 Angle : 0.551 8.603 13587 Z= 0.311 Chirality : 0.034 0.291 1649 Planarity : 0.004 0.060 927 Dihedral : 25.105 179.997 3823 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.75 % Favored : 89.05 % Rotamer: Outliers : 4.20 % Allowed : 32.63 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.56 (0.38), residues: 493 helix: 1.23 (0.41), residues: 168 sheet: -2.18 (0.69), residues: 55 loop : -2.39 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.020 0.001 TYR A 305 PHE 0.017 0.001 PHE A 137 TRP 0.006 0.001 TRP A 278 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 ( 9288) covalent geometry : angle 0.55066 / 0.31 (13584) hydrogen bonds : bond 0.06129 / 3.95 ( 313) hydrogen bonds : angle 3.95801 / 2.64 ( 701) metal coordination : bond 0.01897 / 0.95 ( 4) metal coordination : angle 1.13192 / 0.57 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8206 (ttmt) REVERT: A 193 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8165 (mm) REVERT: A 203 ASN cc_start: 0.8888 (t0) cc_final: 0.8531 (t0) REVERT: A 207 GLN cc_start: 0.8386 (tp-100) cc_final: 0.8109 (tp-100) REVERT: A 210 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: A 292 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8894 (tptp) REVERT: A 356 LYS cc_start: 0.9305 (mmmm) cc_final: 0.8894 (mmmm) outliers start: 18 outliers final: 14 residues processed: 60 average time/residue: 0.0747 time to fit residues: 6.4571 Evaluate side-chains 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 GLN ** 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 = 0.3750 r_free = 0.3750 target = 0.083350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061505 restraints weight = 31213.202| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.54 r_work: 0.3096 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9292 Z= 0.129 Angle : 0.536 10.226 13587 Z= 0.301 Chirality : 0.033 0.295 1649 Planarity : 0.004 0.062 927 Dihedral : 25.065 179.846 3823 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.55 % Favored : 89.25 % Rotamer: Outliers : 4.43 % Allowed : 31.93 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.50 (0.38), residues: 493 helix: 1.23 (0.41), residues: 168 sheet: -2.13 (0.69), residues: 55 loop : -2.34 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 37 TYR 0.016 0.001 TYR A 305 PHE 0.007 0.001 PHE A 318 TRP 0.006 0.001 TRP A 478 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 ( 9288) covalent geometry : angle 0.53571 / 0.30 (13584) hydrogen bonds : bond 0.05683 / 3.68 ( 313) hydrogen bonds : angle 3.88154 / 2.58 ( 701) metal coordination : bond 0.01481 / 0.74 ( 4) metal coordination : angle 0.92276 / 0.47 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1663.73 seconds wall clock time: 29 minutes 17.69 seconds (1757.69 seconds total)