Starting phenix.real_space_refine on Wed Feb 4 03:32:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lis_63122/02_2026/9lis_63122.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lis_63122/02_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_63122/02_2026/9lis_63122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lis_63122/02_2026/9lis_63122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lis_63122/02_2026/9lis_63122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lis_63122/02_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-2.0-5952/lib/python3.9/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: 2.15, 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: 0.68 Conformation dependent library (CDL) restraints added in 147.5 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: 1.30 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: 1.85 Time building geometry restraints manager: 0.91 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=" CB LYS A 355 " pdb=" CG LYS A 355 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" CG1 ILE A 335 " pdb=" CD1 ILE A 335 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 bond pdb=" CG ARG A 480 " pdb=" CD ARG A 480 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CA LYS A 392 " pdb=" CB LYS A 392 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.08e+00 ... (remaining 9283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 13144 1.68 - 3.35: 348 3.35 - 5.03: 66 5.03 - 6.71: 20 6.71 - 8.39: 6 Bond angle restraints: 13584 Sorted by residual: angle pdb=" CB LYS A 355 " pdb=" CG LYS A 355 " pdb=" CD LYS A 355 " ideal model delta sigma weight residual 111.30 119.59 -8.29 2.30e+00 1.89e-01 1.30e+01 angle pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " pdb=" CD GLU A 223 " ideal model delta sigma weight residual 112.60 118.58 -5.98 1.70e+00 3.46e-01 1.24e+01 angle pdb=" C GLY A 391 " pdb=" N LYS A 392 " pdb=" CA LYS A 392 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" CA LYS A 392 " pdb=" CB LYS A 392 " pdb=" CG LYS A 392 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA GLU A 223 " pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.50e+00 ... (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: 1409 0.047 - 0.095: 207 0.095 - 0.142: 23 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.130 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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= 0.186 Angle : 0.703 8.385 13587 Z= 0.358 Chirality : 0.036 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 covalent geometry : bond 0.00375 ( 9288) covalent geometry : angle 0.70307 (13584) hydrogen bonds : bond 0.13574 ( 313) hydrogen bonds : angle 6.14083 ( 701) metal coordination : bond 0.02047 ( 4) metal coordination : angle 1.27079 ( 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 : 0.175 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: 0.0826 time to fit residues: 6.3904 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 : 0.208 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3642 r_free = 0.3642 target = 0.078028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055755 restraints weight = 32511.286| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.68 r_work: 0.2957 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.127 9292 Z= 0.439 Angle : 0.803 9.025 13587 Z= 0.412 Chirality : 0.042 0.233 1649 Planarity : 0.006 0.067 927 Dihedral : 25.322 179.926 3832 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.98 % Favored : 86.82 % Rotamer: Outliers : 7.69 % Allowed : 28.21 % 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: -1.91 (0.37), residues: 493 helix: 0.77 (0.40), residues: 162 sheet: -2.43 (0.56), residues: 77 loop : -2.32 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 213 TYR 0.022 0.002 TYR A 305 PHE 0.016 0.002 PHE A 453 TRP 0.004 0.001 TRP A 478 HIS 0.006 0.002 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00885 ( 9288) covalent geometry : angle 0.80153 (13584) hydrogen bonds : bond 0.07609 ( 313) hydrogen bonds : angle 4.76033 ( 701) metal coordination : bond 0.03220 ( 4) metal coordination : angle 3.75580 ( 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: 33 poor density : 38 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 356 LYS cc_start: 0.9360 (mmmm) cc_final: 0.9017 (mmmm) REVERT: A 402 MET cc_start: 0.7719 (mmm) cc_final: 0.7512 (mmm) REVERT: A 420 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8292 (t0) outliers start: 33 outliers final: 18 residues processed: 67 average time/residue: 0.0745 time to fit residues: 7.2967 Evaluate side-chains 55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 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 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 351 LEU 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 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: 10.0000 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.082335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060212 restraints weight = 31321.443| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.52 r_work: 0.3069 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9292 Z= 0.140 Angle : 0.602 7.104 13587 Z= 0.310 Chirality : 0.033 0.253 1649 Planarity : 0.005 0.061 927 Dihedral : 25.061 178.687 3826 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.53 % Favored : 90.26 % Rotamer: Outliers : 5.13 % Allowed : 29.60 % Favored : 65.27 % 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: -1.32 (0.39), residues: 493 helix: 1.37 (0.41), residues: 162 sheet: -1.90 (0.62), residues: 77 loop : -2.12 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.008 0.001 TYR A 305 PHE 0.007 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 covalent geometry : bond 0.00287 ( 9288) covalent geometry : angle 0.60213 (13584) hydrogen bonds : bond 0.04985 ( 313) hydrogen bonds : angle 4.03938 ( 701) metal coordination : bond 0.01528 ( 4) metal coordination : angle 1.11439 ( 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 69 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8245 (ttt180) REVERT: A 203 ASN cc_start: 0.8792 (t0) cc_final: 0.8451 (t0) REVERT: A 210 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8633 (tm-30) REVERT: A 292 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8853 (tptp) REVERT: A 356 LYS cc_start: 0.9282 (mmmm) cc_final: 0.8910 (mmmm) outliers start: 22 outliers final: 14 residues processed: 63 average time/residue: 0.0998 time to fit residues: 8.7993 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 : 0.212 ------------------------------------------------------------------------------- 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 63 ARG 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 210 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 248 VAL 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 357 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 421 VAL 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: 7.9990 chunk 31 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 37 optimal weight: 0.0770 chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3685 r_free = 0.3685 target = 0.080093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057532 restraints weight = 32769.021| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.56 r_work: 0.3001 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9292 Z= 0.262 Angle : 0.650 6.728 13587 Z= 0.336 Chirality : 0.036 0.264 1649 Planarity : 0.005 0.059 927 Dihedral : 25.144 179.654 3823 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.16 % Favored : 88.64 % Rotamer: Outliers : 6.99 % Allowed : 29.60 % Favored : 63.40 % 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: 1.26 (0.41), residues: 162 sheet: -1.96 (0.62), residues: 77 loop : -2.22 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.014 0.001 TYR A 305 PHE 0.010 0.001 PHE A 453 TRP 0.003 0.001 TRP A 478 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 9288) covalent geometry : angle 0.64929 (13584) hydrogen bonds : bond 0.06066 ( 313) hydrogen bonds : angle 4.12611 ( 701) metal coordination : bond 0.02449 ( 4) metal coordination : angle 2.25961 ( 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 73 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8290 (mm) REVERT: A 203 ASN cc_start: 0.8819 (t0) cc_final: 0.8450 (t0) REVERT: A 210 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8643 (tm-30) REVERT: A 356 LYS cc_start: 0.9324 (mmmm) cc_final: 0.8964 (mmmm) REVERT: A 402 MET cc_start: 0.7651 (mmm) cc_final: 0.7344 (mmm) REVERT: A 420 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8311 (t0) REVERT: A 483 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.5812 (pt0) outliers start: 30 outliers final: 19 residues processed: 67 average time/residue: 0.0890 time to fit residues: 8.6064 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 : 0.192 ------------------------------------------------------------------------------- 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 52 THR 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 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 313 MET 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 483 GLN 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: 20.0000 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 chunk 47 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 2.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3699 r_free = 0.3699 target = 0.080812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058276 restraints weight = 32468.635| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.55 r_work: 0.3015 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 9292 Z= 0.217 Angle : 0.617 6.576 13587 Z= 0.320 Chirality : 0.035 0.280 1649 Planarity : 0.005 0.059 927 Dihedral : 25.151 179.462 3823 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.95 % Favored : 88.84 % Rotamer: Outliers : 4.90 % Allowed : 31.24 % 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: -1.54 (0.39), residues: 493 helix: 1.31 (0.41), residues: 162 sheet: -2.46 (0.54), residues: 92 loop : -2.12 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.012 0.001 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 379 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 9288) covalent geometry : angle 0.61624 (13584) hydrogen bonds : bond 0.05670 ( 313) hydrogen bonds : angle 4.06045 ( 701) metal coordination : bond 0.02270 ( 4) metal coordination : angle 1.73475 ( 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 66 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8284 (mm) REVERT: A 203 ASN cc_start: 0.8877 (t0) cc_final: 0.8510 (t0) REVERT: A 213 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8421 (mtm-85) REVERT: A 292 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8932 (tptp) REVERT: A 356 LYS cc_start: 0.9338 (mmmm) cc_final: 0.8962 (mmmm) REVERT: A 402 MET cc_start: 0.7653 (mmm) cc_final: 0.7247 (mmm) REVERT: A 420 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8090 (t0) outliers start: 21 outliers final: 16 residues processed: 62 average time/residue: 0.0908 time to fit residues: 7.9040 Evaluate side-chains 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 142 CYS 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 248 VAL Chi-restraints excluded: chain A residue 279 GLU 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 345 CYS 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 421 VAL 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: 3.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 40 optimal weight: 0.0370 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3740 r_free = 0.3740 target = 0.082790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.060343 restraints weight = 32051.015| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.54 r_work: 0.3072 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9292 Z= 0.150 Angle : 0.584 9.730 13587 Z= 0.300 Chirality : 0.033 0.303 1649 Planarity : 0.004 0.059 927 Dihedral : 25.041 179.567 3823 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.76 % Favored : 88.03 % Rotamer: Outliers : 4.66 % Allowed : 30.07 % Favored : 65.27 % 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: -1.40 (0.39), residues: 493 helix: 1.28 (0.42), residues: 168 sheet: -2.07 (0.70), residues: 55 loop : -2.24 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.007 0.001 TYR A 305 PHE 0.012 0.001 PHE A 137 TRP 0.005 0.001 TRP A 478 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9288) covalent geometry : angle 0.58431 (13584) hydrogen bonds : bond 0.05032 ( 313) hydrogen bonds : angle 3.86960 ( 701) metal coordination : bond 0.01850 ( 4) metal coordination : angle 0.81846 ( 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 69 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8229 (mm) REVERT: A 203 ASN cc_start: 0.8892 (t0) cc_final: 0.8564 (t0) REVERT: A 207 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8142 (tp-100) REVERT: A 210 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8590 (tm-30) REVERT: A 292 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8887 (tptp) REVERT: A 356 LYS cc_start: 0.9299 (mmmm) cc_final: 0.8920 (mmmm) REVERT: A 402 MET cc_start: 0.7674 (mmm) cc_final: 0.7295 (mmm) outliers start: 20 outliers final: 15 residues processed: 64 average time/residue: 0.1007 time to fit residues: 8.9891 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 : 0.179 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 279 GLU 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 399 HIS Chi-restraints excluded: chain A residue 421 VAL 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: 20.0000 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3730 r_free = 0.3730 target = 0.082219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.059764 restraints weight = 32242.474| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.55 r_work: 0.3054 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9292 Z= 0.178 Angle : 0.596 6.558 13587 Z= 0.306 Chirality : 0.033 0.300 1649 Planarity : 0.005 0.063 927 Dihedral : 25.060 179.921 3822 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.55 % Favored : 89.25 % Rotamer: Outliers : 4.90 % Allowed : 31.47 % 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: -1.45 (0.38), residues: 493 helix: 1.32 (0.41), residues: 168 sheet: -2.06 (0.70), residues: 55 loop : -2.34 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.016 0.001 TYR A 305 PHE 0.008 0.001 PHE A 453 TRP 0.003 0.001 TRP A 278 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9288) covalent geometry : angle 0.59608 (13584) hydrogen bonds : bond 0.05400 ( 313) hydrogen bonds : angle 3.88933 ( 701) metal coordination : bond 0.02002 ( 4) metal coordination : angle 1.41777 ( 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 66 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8264 (mm) REVERT: A 203 ASN cc_start: 0.8869 (t0) cc_final: 0.8526 (t0) REVERT: A 207 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8120 (tp-100) REVERT: A 210 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: A 292 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8914 (tptp) REVERT: A 356 LYS cc_start: 0.9322 (mmmm) cc_final: 0.8939 (mmmm) REVERT: A 420 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8058 (t0) outliers start: 21 outliers final: 15 residues processed: 61 average time/residue: 0.0882 time to fit residues: 7.6917 Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 279 GLU 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 313 MET 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 421 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: 5.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3655 r_free = 0.3655 target = 0.078749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056180 restraints weight = 32849.060| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.69 r_work: 0.2954 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 0.007 0.117 9292 Z= 0.357 Angle : 0.737 6.777 13587 Z= 0.380 Chirality : 0.040 0.299 1649 Planarity : 0.006 0.059 927 Dihedral : 25.347 179.523 3822 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.37 % Favored : 87.42 % Rotamer: Outliers : 4.43 % Allowed : 31.70 % 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: -1.75 (0.37), residues: 493 helix: 0.93 (0.39), residues: 167 sheet: -1.75 (0.67), residues: 65 loop : -2.54 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 105 TYR 0.015 0.002 TYR A 305 PHE 0.015 0.002 PHE A 318 TRP 0.004 0.001 TRP A 278 HIS 0.006 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00725 ( 9288) covalent geometry : angle 0.73520 (13584) hydrogen bonds : bond 0.07070 ( 313) hydrogen bonds : angle 4.33439 ( 701) metal coordination : bond 0.02869 ( 4) metal coordination : angle 3.64059 ( 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 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 203 ASN cc_start: 0.8890 (t0) cc_final: 0.8527 (t0) REVERT: A 213 ARG cc_start: 0.8929 (mtm-85) cc_final: 0.8415 (mtm-85) REVERT: A 292 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8935 (tptp) REVERT: A 356 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9024 (mmmm) REVERT: A 402 MET cc_start: 0.7715 (mmm) cc_final: 0.7442 (mmm) REVERT: A 420 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8424 (t0) outliers start: 19 outliers final: 13 residues processed: 58 average time/residue: 0.0920 time to fit residues: 7.8299 Evaluate side-chains 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 THR 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 193 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 335 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 495 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.082729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060241 restraints weight = 31853.965| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.55 r_work: 0.3065 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9292 Z= 0.142 Angle : 0.604 6.894 13587 Z= 0.307 Chirality : 0.033 0.321 1649 Planarity : 0.004 0.060 927 Dihedral : 25.108 178.803 3820 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.95 % Favored : 88.84 % Rotamer: Outliers : 4.43 % Allowed : 32.17 % Favored : 63.40 % 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 (0.38), residues: 493 helix: 1.33 (0.41), residues: 167 sheet: -2.09 (0.70), residues: 55 loop : -2.44 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.008 0.001 TYR A 305 PHE 0.006 0.001 PHE A 198 TRP 0.007 0.001 TRP A 478 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9288) covalent geometry : angle 0.60370 (13584) hydrogen bonds : bond 0.04897 ( 313) hydrogen bonds : angle 3.91432 ( 701) metal coordination : bond 0.01627 ( 4) metal coordination : angle 0.82918 ( 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: 19 poor density : 46 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8277 (mm) REVERT: A 203 ASN cc_start: 0.8853 (t0) cc_final: 0.8550 (t0) REVERT: A 213 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8456 (mtm-85) REVERT: A 292 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8911 (tptp) REVERT: A 356 LYS cc_start: 0.9302 (mmmm) cc_final: 0.8895 (mmmm) REVERT: A 402 MET cc_start: 0.7711 (mmm) cc_final: 0.7507 (mmm) outliers start: 19 outliers final: 15 residues processed: 61 average time/residue: 0.0938 time to fit residues: 8.1741 Evaluate side-chains 58 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 CYS 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 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 292 LYS 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 421 VAL 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: 7.9990 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.0670 overall best weight: 1.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3737 r_free = 0.3737 target = 0.082746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.060337 restraints weight = 31968.963| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.54 r_work: 0.3069 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9292 Z= 0.148 Angle : 0.601 6.654 13587 Z= 0.305 Chirality : 0.033 0.326 1649 Planarity : 0.004 0.061 927 Dihedral : 25.076 179.820 3819 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.75 % Favored : 89.05 % Rotamer: Outliers : 2.56 % Allowed : 34.03 % Favored : 63.40 % 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: -1.45 (0.38), residues: 493 helix: 1.34 (0.42), residues: 168 sheet: -2.06 (0.71), residues: 55 loop : -2.36 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 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 173 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9288) covalent geometry : angle 0.60088 (13584) hydrogen bonds : bond 0.04969 ( 313) hydrogen bonds : angle 3.86216 ( 701) metal coordination : bond 0.01732 ( 4) metal coordination : angle 1.15282 ( 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 55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8254 (mm) REVERT: A 203 ASN cc_start: 0.8880 (t0) cc_final: 0.8237 (t0) REVERT: A 206 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8154 (t) REVERT: A 213 ARG cc_start: 0.8888 (mtm-85) cc_final: 0.8435 (mtm-85) REVERT: A 292 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8917 (tptp) REVERT: A 356 LYS cc_start: 0.9310 (mmmm) cc_final: 0.8897 (mmmm) REVERT: A 402 MET cc_start: 0.7690 (mmm) cc_final: 0.7464 (mmm) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 0.0947 time to fit residues: 7.1557 Evaluate side-chains 53 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 279 GLU Chi-restraints excluded: chain A residue 292 LYS 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 421 VAL 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: 0.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.085388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063411 restraints weight = 31698.891| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.53 r_work: 0.3148 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9292 Z= 0.122 Angle : 0.587 10.570 13587 Z= 0.294 Chirality : 0.031 0.325 1649 Planarity : 0.004 0.064 927 Dihedral : 24.906 179.690 3819 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.75 % Favored : 89.05 % Rotamer: Outliers : 3.03 % Allowed : 33.80 % 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: -1.33 (0.39), residues: 493 helix: 1.47 (0.42), residues: 168 sheet: -1.95 (0.74), residues: 50 loop : -2.33 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.010 0.001 TYR A 305 PHE 0.005 0.001 PHE A 236 TRP 0.005 0.001 TRP A 478 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9288) covalent geometry : angle 0.58709 (13584) hydrogen bonds : bond 0.04253 ( 313) hydrogen bonds : angle 3.74497 ( 701) metal coordination : bond 0.01576 ( 4) metal coordination : angle 0.48965 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1969.32 seconds wall clock time: 34 minutes 42.35 seconds (2082.35 seconds total)