Starting phenix.real_space_refine on Wed Aug 5 03:29:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vbg_43124/08_2026/8vbg_43124.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vbg_43124/08_2026/8vbg_43124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vbg_43124/08_2026/8vbg_43124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vbg_43124/08_2026/8vbg_43124.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vbg_43124/08_2026/8vbg_43124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vbg_43124/08_2026/8vbg_43124.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 2 5.21 5 S 13 5.16 5 C 5320 2.51 5 N 1404 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8417 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4400 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 504} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 542, 4400 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 504} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 4512 Chain: "B" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3219 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 28, 'TRANS': 367} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 761 Classifications: {'DNA': 35, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 36} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'F2A': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.95, per 1000 atoms: 0.23 Number of scatterers: 8417 At special positions: 0 Unit cell: (78.48, 94.32, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 13 16.00 P 40 15.00 Mg 2 11.99 O 1638 8.00 N 1404 7.00 C 5320 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: 0.76 Conformation dependent library (CDL) restraints added in 309.2 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 36.6% alpha, 17.4% beta 13 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.545A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 129 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.767A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.200A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.507A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.634A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.589A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 194 through 211 removed outlier: 3.721A pdb=" N GLU B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 removed outlier: 3.847A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 363 through 384 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 354 removed outlier: 8.605A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA8, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.361A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 355 removed outlier: 8.555A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA B 327 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1307 1.30 - 1.43: 2444 1.43 - 1.57: 4862 1.57 - 1.70: 77 1.70 - 1.83: 25 Bond restraints: 8715 Sorted by residual: bond pdb=" C GLY B 190 " pdb=" N SER B 191 " ideal model delta sigma weight residual 1.327 1.458 -0.131 1.47e-02 4.63e+03 7.89e+01 bond pdb=" O3B F2A A 601 " pdb=" PG F2A A 601 " ideal model delta sigma weight residual 1.728 1.611 0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C GLN A 509 " pdb=" O GLN A 509 " ideal model delta sigma weight residual 1.233 1.205 0.028 4.80e-03 4.34e+04 3.39e+01 bond pdb=" C THR A 107 " pdb=" N VAL A 108 " ideal model delta sigma weight residual 1.330 1.416 -0.085 1.48e-02 4.57e+03 3.32e+01 bond pdb=" C GLU A 302 " pdb=" O GLU A 302 " ideal model delta sigma weight residual 1.236 1.175 0.062 1.15e-02 7.56e+03 2.88e+01 ... (remaining 8710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11459 2.49 - 4.98: 474 4.98 - 7.47: 64 7.47 - 9.96: 15 9.96 - 12.45: 6 Bond angle restraints: 12018 Sorted by residual: angle pdb=" N ILE B 159 " pdb=" CA ILE B 159 " pdb=" C ILE B 159 " ideal model delta sigma weight residual 113.10 105.63 7.47 9.70e-01 1.06e+00 5.94e+01 angle pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N VAL A 111 " ideal model delta sigma weight residual 116.37 125.38 -9.01 1.19e+00 7.06e-01 5.73e+01 angle pdb=" C THR B 84 " pdb=" CA THR B 84 " pdb=" CB THR B 84 " ideal model delta sigma weight residual 109.89 121.86 -11.97 1.60e+00 3.91e-01 5.60e+01 angle pdb=" C THR B 409 " pdb=" CA THR B 409 " pdb=" CB THR B 409 " ideal model delta sigma weight residual 109.65 122.10 -12.45 1.74e+00 3.30e-01 5.12e+01 angle pdb=" O ASP A 110 " pdb=" C ASP A 110 " pdb=" N VAL A 111 " ideal model delta sigma weight residual 123.27 114.98 8.29 1.18e+00 7.18e-01 4.93e+01 ... (remaining 12013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.74: 4538 28.74 - 57.48: 514 57.48 - 86.21: 69 86.21 - 114.95: 5 114.95 - 143.69: 1 Dihedral angle restraints: 5127 sinusoidal: 2378 harmonic: 2749 Sorted by residual: dihedral pdb=" C THR A 240 " pdb=" N THR A 240 " pdb=" CA THR A 240 " pdb=" CB THR A 240 " ideal model delta harmonic sigma weight residual -122.00 -106.41 -15.59 0 2.50e+00 1.60e-01 3.89e+01 dihedral pdb=" C THR B 84 " pdb=" N THR B 84 " pdb=" CA THR B 84 " pdb=" CB THR B 84 " ideal model delta harmonic sigma weight residual -122.00 -136.16 14.16 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" C PRO A 537 " pdb=" N PRO A 537 " pdb=" CA PRO A 537 " pdb=" CB PRO A 537 " ideal model delta harmonic sigma weight residual -120.70 -107.17 -13.53 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 5124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1160 0.098 - 0.195: 121 0.195 - 0.293: 28 0.293 - 0.391: 4 0.391 - 0.489: 3 Chirality restraints: 1316 Sorted by residual: chirality pdb=" C3' DG F 33 " pdb=" C4' DG F 33 " pdb=" O3' DG F 33 " pdb=" C2' DG F 33 " both_signs ideal model delta sigma weight residual False -2.73 -2.24 -0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" C3' DT F 18 " pdb=" C4' DT F 18 " pdb=" O3' DT F 18 " pdb=" C2' DT F 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.31 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA THR B 84 " pdb=" N THR B 84 " pdb=" C THR B 84 " pdb=" CB THR B 84 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 1313 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 110 " 0.023 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ASP A 110 " -0.074 2.00e-02 2.50e+03 pdb=" O ASP A 110 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL A 111 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG F 33 " -0.059 2.00e-02 2.50e+03 2.29e-02 1.57e+01 pdb=" N9 DG F 33 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG F 33 " 0.020 2.00e-02 2.50e+03 pdb=" N7 DG F 33 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DG F 33 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG F 33 " -0.020 2.00e-02 2.50e+03 pdb=" O6 DG F 33 " -0.022 2.00e-02 2.50e+03 pdb=" N1 DG F 33 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG F 33 " 0.010 2.00e-02 2.50e+03 pdb=" N2 DG F 33 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG F 33 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DG F 33 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 302 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU A 302 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU A 302 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU A 303 " 0.023 2.00e-02 2.50e+03 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 173 2.65 - 3.22: 7149 3.22 - 3.78: 14463 3.78 - 4.34: 20146 4.34 - 4.90: 31139 Nonbonded interactions: 73070 Sorted by model distance: nonbonded pdb=" OD2 ASP A 185 " pdb="MG MG A 602 " model vdw 2.092 2.170 nonbonded pdb=" NH2 ARG A 358 " pdb=" OE2 GLU B 396 " model vdw 2.222 3.120 nonbonded pdb=" N GLU B 396 " pdb=" OE1 GLU B 396 " model vdw 2.247 3.120 nonbonded pdb=" O LEU A 80 " pdb=" OG1 THR A 84 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP A 110 " pdb="MG MG A 602 " model vdw 2.340 2.170 ... (remaining 73065 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=0.49 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: 0.010 Normalize map: mean=0, sd=1: 4.030 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 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 : 0.007 0.131 8715 Z= 0.503 Angle : 1.089 12.451 12018 Z= 0.747 Chirality : 0.071 0.489 1316 Planarity : 0.005 0.043 1381 Dihedral : 21.841 143.687 3353 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.76 % Favored : 95.16 % Rotamer: Outliers : 7.51 % Allowed : 23.00 % Favored : 69.49 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.28), residues: 931 helix: 0.94 (0.31), residues: 308 sheet: -0.47 (0.37), residues: 175 loop : -0.45 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.018 0.002 TYR A 501 PHE 0.016 0.002 PHE B 171 TRP 0.045 0.002 TRP A 406 HIS 0.006 0.002 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.50 ( 8715) covalent geometry : angle 1.08905 / 0.75 (12018) hydrogen bonds : bond 0.13446 / 9.07 ( 361) hydrogen bonds : angle 6.12654 / 4.48 ( 969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 84 time to evaluate : 0.263 Fit side-chains REVERT: A 67 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (t0) REVERT: A 454 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6430 (ttpt) REVERT: A 500 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7951 (mp10) REVERT: A 537 PRO cc_start: 0.8472 (OUTLIER) cc_final: 0.8195 (Cg_endo) REVERT: B 242 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.7104 (mt0) REVERT: B 277 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8106 (tmt-80) REVERT: B 281 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7718 (mmpt) outliers start: 61 outliers final: 16 residues processed: 130 average time/residue: 0.5369 time to fit residues: 74.1301 Evaluate side-chains 91 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 537 PRO Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.0670 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN A 539 HIS B 96 HIS B 182 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.102421 restraints weight = 16431.913| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.53 r_work: 0.3251 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8715 Z= 0.148 Angle : 0.608 8.860 12018 Z= 0.327 Chirality : 0.045 0.303 1316 Planarity : 0.005 0.075 1381 Dihedral : 17.561 141.122 1456 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.87 % Favored : 95.91 % Rotamer: Outliers : 4.12 % Allowed : 24.33 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.28), residues: 931 helix: 1.61 (0.30), residues: 318 sheet: -0.36 (0.39), residues: 165 loop : -0.20 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 358 TYR 0.019 0.002 TYR A 457 PHE 0.014 0.002 PHE A 440 TRP 0.033 0.001 TRP A 406 HIS 0.011 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 8715) covalent geometry : angle 0.60807 / 0.33 (12018) hydrogen bonds : bond 0.04000 / 2.70 ( 361) hydrogen bonds : angle 4.52642 / 3.23 ( 969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.185 Fit side-chains REVERT: A 454 LYS cc_start: 0.7132 (mtmm) cc_final: 0.6243 (ttpt) REVERT: A 500 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7752 (mp10) REVERT: A 520 GLN cc_start: 0.8699 (mt0) cc_final: 0.8478 (mt0) REVERT: B 242 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6841 (mt0) REVERT: B 277 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8203 (tmt170) REVERT: B 356 ARG cc_start: 0.7663 (tpm-80) cc_final: 0.7183 (tpp-160) REVERT: B 425 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7418 (pp) outliers start: 32 outliers final: 13 residues processed: 111 average time/residue: 0.5087 time to fit residues: 60.1115 Evaluate side-chains 87 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 494 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101705 restraints weight = 14864.667| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.40 r_work: 0.3239 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8715 Z= 0.159 Angle : 0.578 8.224 12018 Z= 0.310 Chirality : 0.044 0.325 1316 Planarity : 0.004 0.064 1381 Dihedral : 16.970 141.699 1437 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 3.63 % Allowed : 24.82 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.28), residues: 931 helix: 1.81 (0.30), residues: 319 sheet: -0.50 (0.37), residues: 171 loop : -0.16 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 358 TYR 0.020 0.002 TYR A 457 PHE 0.009 0.001 PHE A 160 TRP 0.031 0.001 TRP A 406 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 8715) covalent geometry : angle 0.57841 / 0.31 (12018) hydrogen bonds : bond 0.03779 / 2.56 ( 361) hydrogen bonds : angle 4.35967 / 3.09 ( 969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8574 (mppt) REVERT: A 64 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7962 (mtpp) REVERT: A 431 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8588 (mtpp) REVERT: A 454 LYS cc_start: 0.7219 (mtmm) cc_final: 0.6342 (ttpt) REVERT: A 461 LYS cc_start: 0.8690 (mptt) cc_final: 0.8449 (mptt) REVERT: A 500 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7742 (mp10) REVERT: A 542 ILE cc_start: 0.5089 (OUTLIER) cc_final: 0.4781 (mp) REVERT: B 242 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6936 (mt0) REVERT: B 277 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8370 (ttp80) REVERT: B 326 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8490 (mt) REVERT: B 356 ARG cc_start: 0.7521 (tpm-80) cc_final: 0.6998 (tpp80) REVERT: B 425 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7434 (pp) outliers start: 28 outliers final: 10 residues processed: 90 average time/residue: 0.5762 time to fit residues: 55.0140 Evaluate side-chains 81 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.133144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099576 restraints weight = 14942.556| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.40 r_work: 0.3210 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8715 Z= 0.212 Angle : 0.590 7.265 12018 Z= 0.318 Chirality : 0.045 0.308 1316 Planarity : 0.005 0.068 1381 Dihedral : 16.758 143.243 1425 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 3.75 % Allowed : 24.58 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.28), residues: 931 helix: 1.73 (0.29), residues: 319 sheet: -0.60 (0.36), residues: 171 loop : -0.20 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 358 TYR 0.019 0.002 TYR A 457 PHE 0.011 0.002 PHE A 160 TRP 0.037 0.002 TRP A 406 HIS 0.006 0.002 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 8715) covalent geometry : angle 0.58959 / 0.32 (12018) hydrogen bonds : bond 0.03992 / 2.70 ( 361) hydrogen bonds : angle 4.36946 / 3.10 ( 969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.220 Fit side-chains REVERT: A 16 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7559 (mtt) REVERT: A 431 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8620 (mtpp) REVERT: A 454 LYS cc_start: 0.7247 (mtmm) cc_final: 0.6342 (ttpt) REVERT: A 500 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7719 (mp10) REVERT: B 16 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7203 (mtp) REVERT: B 242 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6985 (mt0) REVERT: B 277 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8366 (ttp80) REVERT: B 326 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8516 (mt) REVERT: B 356 ARG cc_start: 0.7517 (tpm-80) cc_final: 0.7007 (tpp80) REVERT: B 425 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7516 (pp) outliers start: 29 outliers final: 12 residues processed: 92 average time/residue: 0.4999 time to fit residues: 48.7950 Evaluate side-chains 80 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 0.7980 chunk 91 optimal weight: 0.0170 chunk 18 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 43 optimal weight: 0.0050 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.136853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104304 restraints weight = 14615.246| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.35 r_work: 0.3282 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8715 Z= 0.118 Angle : 0.535 7.268 12018 Z= 0.289 Chirality : 0.043 0.330 1316 Planarity : 0.004 0.076 1381 Dihedral : 16.404 140.765 1424 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.27 % Allowed : 25.67 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 931 helix: 2.06 (0.29), residues: 319 sheet: -0.47 (0.37), residues: 165 loop : -0.08 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 358 TYR 0.023 0.001 TYR A 457 PHE 0.010 0.001 PHE B 61 TRP 0.046 0.001 TRP A 406 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 8715) covalent geometry : angle 0.53539 / 0.29 (12018) hydrogen bonds : bond 0.03290 / 2.23 ( 361) hydrogen bonds : angle 4.18790 / 2.97 ( 969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.189 Fit side-chains REVERT: A 16 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7501 (mtt) REVERT: A 431 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8568 (mtpp) REVERT: A 454 LYS cc_start: 0.7222 (mtmm) cc_final: 0.6394 (ttpt) REVERT: A 461 LYS cc_start: 0.8685 (mptt) cc_final: 0.8438 (mptt) REVERT: A 500 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7682 (mp10) REVERT: B 16 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7059 (mtp) REVERT: B 242 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7081 (mt0) REVERT: B 277 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8352 (ttp80) REVERT: B 356 ARG cc_start: 0.7428 (tpm-80) cc_final: 0.6966 (tpp80) REVERT: B 425 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7433 (pp) outliers start: 25 outliers final: 7 residues processed: 91 average time/residue: 0.4748 time to fit residues: 46.1486 Evaluate side-chains 75 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 494 ASN A 498 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.134398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100888 restraints weight = 15684.890| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.46 r_work: 0.3231 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8715 Z= 0.177 Angle : 0.560 7.223 12018 Z= 0.301 Chirality : 0.044 0.317 1316 Planarity : 0.005 0.085 1381 Dihedral : 16.355 142.899 1422 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.78 % Allowed : 25.42 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.28), residues: 931 helix: 2.19 (0.30), residues: 313 sheet: -0.47 (0.36), residues: 171 loop : -0.07 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 358 TYR 0.021 0.002 TYR A 457 PHE 0.012 0.001 PHE A 160 TRP 0.047 0.001 TRP A 406 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 8715) covalent geometry : angle 0.56032 / 0.30 (12018) hydrogen bonds : bond 0.03654 / 2.48 ( 361) hydrogen bonds : angle 4.22637 / 3.01 ( 969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.217 Fit side-chains REVERT: A 16 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7520 (mtt) REVERT: A 431 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8655 (mtpt) REVERT: A 454 LYS cc_start: 0.7219 (mtmm) cc_final: 0.6352 (ttpt) REVERT: A 500 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7691 (mp10) REVERT: B 277 ARG cc_start: 0.8615 (ttp-110) cc_final: 0.8371 (ttp80) REVERT: B 326 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8513 (mt) REVERT: B 356 ARG cc_start: 0.7432 (tpm-80) cc_final: 0.6961 (tpp80) REVERT: B 425 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7483 (pp) outliers start: 21 outliers final: 8 residues processed: 81 average time/residue: 0.4851 time to fit residues: 41.9962 Evaluate side-chains 76 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 74 optimal weight: 0.0030 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.101545 restraints weight = 20535.351| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.79 r_work: 0.3231 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8715 Z= 0.142 Angle : 0.545 7.172 12018 Z= 0.294 Chirality : 0.043 0.321 1316 Planarity : 0.005 0.094 1381 Dihedral : 16.120 142.118 1415 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.94 % Allowed : 25.91 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 931 helix: 2.26 (0.30), residues: 313 sheet: -0.42 (0.36), residues: 171 loop : -0.01 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 358 TYR 0.022 0.001 TYR A 457 PHE 0.009 0.001 PHE B 61 TRP 0.050 0.001 TRP A 406 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 8715) covalent geometry : angle 0.54485 / 0.29 (12018) hydrogen bonds : bond 0.03432 / 2.34 ( 361) hydrogen bonds : angle 4.17476 / 2.98 ( 969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.199 Fit side-chains REVERT: A 16 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7318 (mtt) REVERT: A 431 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8589 (mtpt) REVERT: A 454 LYS cc_start: 0.7254 (mtmm) cc_final: 0.6368 (ttpt) REVERT: A 461 LYS cc_start: 0.8647 (mptt) cc_final: 0.8418 (mptt) REVERT: A 500 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7595 (mp10) REVERT: A 530 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8217 (mtpm) REVERT: B 277 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8398 (ttp80) REVERT: B 356 ARG cc_start: 0.7308 (tpm-80) cc_final: 0.6904 (tpp80) REVERT: B 425 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7507 (pp) outliers start: 14 outliers final: 5 residues processed: 79 average time/residue: 0.6274 time to fit residues: 52.6030 Evaluate side-chains 74 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 494 ASN A 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.133885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099472 restraints weight = 21991.089| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.87 r_work: 0.3191 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8715 Z= 0.189 Angle : 0.570 7.153 12018 Z= 0.308 Chirality : 0.044 0.315 1316 Planarity : 0.005 0.091 1381 Dihedral : 16.147 143.180 1413 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 1.94 % Allowed : 26.51 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 931 helix: 2.23 (0.30), residues: 313 sheet: -0.44 (0.36), residues: 171 loop : -0.01 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 358 TYR 0.021 0.002 TYR A 457 PHE 0.012 0.001 PHE A 160 TRP 0.056 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 ( 8715) covalent geometry : angle 0.57000 / 0.31 (12018) hydrogen bonds : bond 0.03738 / 2.54 ( 361) hydrogen bonds : angle 4.24485 / 3.03 ( 969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.307 Fit side-chains REVERT: A 16 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7354 (mtt) REVERT: A 431 LYS cc_start: 0.8890 (mtmm) cc_final: 0.8605 (mtpt) REVERT: A 454 LYS cc_start: 0.7306 (mtmm) cc_final: 0.6385 (ttpt) REVERT: A 530 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8035 (mtpm) REVERT: B 277 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8396 (ttp80) REVERT: B 326 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8499 (mt) REVERT: B 356 ARG cc_start: 0.7316 (tpm-80) cc_final: 0.6830 (tpp80) REVERT: B 425 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7538 (pp) outliers start: 14 outliers final: 6 residues processed: 77 average time/residue: 0.4679 time to fit residues: 38.5049 Evaluate side-chains 75 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 0.0670 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 ASN B 242 GLN B 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096733 restraints weight = 15269.492| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.63 r_work: 0.3086 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8715 Z= 0.137 Angle : 0.548 7.146 12018 Z= 0.296 Chirality : 0.043 0.323 1316 Planarity : 0.005 0.100 1381 Dihedral : 16.072 142.034 1411 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 1.57 % Allowed : 27.00 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.08 (0.28), residues: 931 helix: 2.36 (0.30), residues: 314 sheet: -0.38 (0.37), residues: 171 loop : 0.06 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 358 TYR 0.023 0.001 TYR A 457 PHE 0.010 0.001 PHE B 61 TRP 0.057 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 8715) covalent geometry : angle 0.54774 / 0.30 (12018) hydrogen bonds : bond 0.03396 / 2.31 ( 361) hydrogen bonds : angle 4.18808 / 3.00 ( 969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.324 Fit side-chains REVERT: A 16 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7511 (mtt) REVERT: A 431 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8580 (mtpt) REVERT: A 454 LYS cc_start: 0.7076 (mtmm) cc_final: 0.6159 (ttpt) REVERT: A 461 LYS cc_start: 0.8542 (mptt) cc_final: 0.8311 (mptt) REVERT: B 207 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7149 (mm-40) REVERT: B 277 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8387 (ttp80) REVERT: B 284 ARG cc_start: 0.6884 (mtt-85) cc_final: 0.6662 (mtp85) REVERT: B 356 ARG cc_start: 0.7287 (tpm-80) cc_final: 0.6745 (tpp80) REVERT: B 425 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7486 (pp) outliers start: 11 outliers final: 6 residues processed: 78 average time/residue: 0.4788 time to fit residues: 39.9920 Evaluate side-chains 76 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 494 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092660 restraints weight = 20612.109| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.03 r_work: 0.3011 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8715 Z= 0.231 Angle : 0.609 11.248 12018 Z= 0.326 Chirality : 0.046 0.309 1316 Planarity : 0.005 0.101 1381 Dihedral : 16.251 144.022 1411 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % Rotamer: Outliers : 2.06 % Allowed : 26.39 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.28), residues: 931 helix: 2.17 (0.29), residues: 313 sheet: -0.47 (0.36), residues: 171 loop : -0.04 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 358 TYR 0.020 0.002 TYR A 457 PHE 0.013 0.002 PHE A 160 TRP 0.061 0.002 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 ( 8715) covalent geometry : angle 0.60854 / 0.33 (12018) hydrogen bonds : bond 0.03996 / 2.71 ( 361) hydrogen bonds : angle 4.32548 / 3.08 ( 969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.235 Fit side-chains REVERT: A 16 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7475 (mtt) REVERT: A 413 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: A 431 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8546 (mtpt) REVERT: A 454 LYS cc_start: 0.7151 (mtmm) cc_final: 0.6183 (ttpt) REVERT: A 461 LYS cc_start: 0.8570 (mptt) cc_final: 0.8345 (mptt) REVERT: A 530 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7858 (mtpm) REVERT: B 277 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8404 (ttp80) REVERT: B 284 ARG cc_start: 0.6912 (mtt-85) cc_final: 0.6686 (mtp85) REVERT: B 356 ARG cc_start: 0.7250 (tpm-80) cc_final: 0.6732 (tpp80) REVERT: B 425 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7496 (pp) outliers start: 15 outliers final: 7 residues processed: 75 average time/residue: 0.5232 time to fit residues: 41.8756 Evaluate side-chains 73 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.0170 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097938 restraints weight = 11723.765| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.30 r_work: 0.3115 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8715 Z= 0.131 Angle : 0.557 9.335 12018 Z= 0.299 Chirality : 0.043 0.328 1316 Planarity : 0.005 0.110 1381 Dihedral : 16.129 141.513 1411 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 1.57 % Allowed : 26.76 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.09 (0.28), residues: 931 helix: 2.39 (0.30), residues: 313 sheet: -0.35 (0.37), residues: 165 loop : 0.02 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 358 TYR 0.024 0.001 TYR A 457 PHE 0.010 0.001 PHE B 61 TRP 0.053 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 8715) covalent geometry : angle 0.55713 / 0.30 (12018) hydrogen bonds : bond 0.03370 / 2.29 ( 361) hydrogen bonds : angle 4.19206 / 3.00 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3531.17 seconds wall clock time: 60 minutes 41.30 seconds (3641.30 seconds total)