Starting phenix.real_space_refine on Thu Oct 22 20:41:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/32qb_59066/10_2026/32qb_59066.cif Found real_map, /net/cci-nas-00/data/ceres_data/32qb_59066/10_2026/32qb_59066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/32qb_59066/10_2026/32qb_59066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/32qb_59066/10_2026/32qb_59066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/32qb_59066/10_2026/32qb_59066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/32qb_59066/10_2026/32qb_59066.map" } resolution = 2.85 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 3539 2.51 5 N 804 2.21 5 O 877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5248 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1108 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "B" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3812 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'ERG': 2, 'NKN': 1, 'Y01': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 1.26, per 1000 atoms: 0.24 Number of scatterers: 5248 At special positions: 0 Unit cell: (95.68, 64.896, 94.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 877 8.00 N 804 7.00 C 3539 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: 0.47 Conformation dependent library (CDL) restraints added in 192.8 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 removed outlier: 3.973A pdb=" N PHE A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 65 removed outlier: 3.878A pdb=" N LEU A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 87 Proline residue: A 76 - end of helix removed outlier: 3.780A pdb=" N TYR A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 134 removed outlier: 5.608A pdb=" N GLY A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 80 removed outlier: 3.709A pdb=" N VAL B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 77 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 93 removed outlier: 4.255A pdb=" N SER B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 removed outlier: 3.597A pdb=" N ASN B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 3.892A pdb=" N GLY B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 146 removed outlier: 4.099A pdb=" N VAL B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 Processing helix chain 'B' and resid 165 through 178 removed outlier: 4.252A pdb=" N ALA B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 4.508A pdb=" N GLY B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 214 removed outlier: 4.699A pdb=" N ALA B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 237 removed outlier: 4.246A pdb=" N PHE B 219 " --> pdb=" O TRP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.545A pdb=" N VAL B 263 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.758A pdb=" N LYS B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 329 removed outlier: 3.609A pdb=" N SER B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.731A pdb=" N LEU B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 385 Processing helix chain 'B' and resid 388 through 399 removed outlier: 4.057A pdb=" N ARG B 394 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 403 Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 413 through 435 removed outlier: 3.621A pdb=" N THR B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.746A pdb=" N PHE B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 467 removed outlier: 3.790A pdb=" N THR B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 500 removed outlier: 4.699A pdb=" N SER B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 519 through 539 removed outlier: 3.901A pdb=" N LEU B 523 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU B 529 " --> pdb=" O ARG B 525 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 789 1.32 - 1.44: 1406 1.44 - 1.57: 3157 1.57 - 1.69: 1 1.69 - 1.81: 37 Bond restraints: 5390 Sorted by residual: bond pdb=" OAB NKN B 607 " pdb=" PAC NKN B 607 " ideal model delta sigma weight residual 1.668 1.508 0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" OAA NKN B 607 " pdb=" PAC NKN B 607 " ideal model delta sigma weight residual 1.667 1.509 0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" C SER B 165 " pdb=" O SER B 165 " ideal model delta sigma weight residual 1.244 1.214 0.030 9.80e-03 1.04e+04 9.17e+00 bond pdb=" N ILE B 164 " pdb=" CA ILE B 164 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.28e-02 6.10e+03 7.93e+00 bond pdb=" N LYS B 401 " pdb=" CA LYS B 401 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.27e-02 6.20e+03 7.76e+00 ... (remaining 5385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.01: 7357 11.01 - 22.03: 2 22.03 - 33.04: 0 33.04 - 44.05: 0 44.05 - 55.06: 1 Bond angle restraints: 7360 Sorted by residual: angle pdb=" OAA NKN B 607 " pdb=" PAC NKN B 607 " pdb=" OAB NKN B 607 " ideal model delta sigma weight residual 54.49 109.55 -55.06 3.00e+00 1.11e-01 3.37e+02 angle pdb=" OAB NKN B 607 " pdb=" PAC NKN B 607 " pdb=" OAD NKN B 607 " ideal model delta sigma weight residual 128.49 109.54 18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" OAA NKN B 607 " pdb=" PAC NKN B 607 " pdb=" OAD NKN B 607 " ideal model delta sigma weight residual 128.00 109.48 18.52 3.00e+00 1.11e-01 3.81e+01 angle pdb=" N ALA B 161 " pdb=" CA ALA B 161 " pdb=" C ALA B 161 " ideal model delta sigma weight residual 111.02 116.66 -5.64 1.22e+00 6.72e-01 2.14e+01 angle pdb=" N GLY B 248 " pdb=" CA GLY B 248 " pdb=" C GLY B 248 " ideal model delta sigma weight residual 114.85 109.10 5.75 1.35e+00 5.49e-01 1.81e+01 ... (remaining 7355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.60: 3420 20.60 - 41.19: 131 41.19 - 61.79: 42 61.79 - 82.39: 10 82.39 - 102.98: 1 Dihedral angle restraints: 3604 sinusoidal: 1784 harmonic: 1820 Sorted by residual: dihedral pdb=" CA LEU B 235 " pdb=" C LEU B 235 " pdb=" N ILE B 236 " pdb=" CA ILE B 236 " ideal model delta harmonic sigma weight residual -180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL A 89 " pdb=" C VAL A 89 " pdb=" N GLN A 90 " pdb=" CA GLN A 90 " ideal model delta harmonic sigma weight residual -180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CBC Y01 A 201 " pdb=" CAR Y01 A 201 " pdb=" CAT Y01 A 201 " pdb=" CBH Y01 A 201 " ideal model delta sinusoidal sigma weight residual -57.13 45.85 -102.98 1 3.00e+01 1.11e-03 1.31e+01 ... (remaining 3601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 743 0.058 - 0.116: 115 0.116 - 0.174: 15 0.174 - 0.231: 1 0.231 - 0.289: 1 Chirality restraints: 875 Sorted by residual: chirality pdb=" CAH NKN B 607 " pdb=" CAG NKN B 607 " pdb=" CAI NKN B 607 " pdb=" OAY NKN B 607 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LEU B 159 " pdb=" N LEU B 159 " pdb=" C LEU B 159 " pdb=" CB LEU B 159 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA LEU A 54 " pdb=" N LEU A 54 " pdb=" C LEU A 54 " pdb=" CB LEU A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 872 not shown) Planarity restraints: 854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 126 " 0.190 9.50e-02 1.11e+02 8.55e-02 5.40e+00 pdb=" NE ARG B 126 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 126 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 126 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 126 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 160 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C GLN B 160 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN B 160 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA B 161 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 157 " 0.160 9.50e-02 1.11e+02 7.24e-02 4.31e+00 pdb=" NE ARG B 157 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 157 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 157 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 157 " -0.000 2.00e-02 2.50e+03 ... (remaining 851 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1197 2.80 - 3.33: 5245 3.33 - 3.85: 8355 3.85 - 4.38: 10275 4.38 - 4.90: 18033 Nonbonded interactions: 43105 Sorted by model distance: nonbonded pdb=" CD1 LEU B 144 " pdb=" OE1 GLN B 160 " model vdw 2.277 3.460 nonbonded pdb=" NH1 ARG B 184 " pdb=" OD1 ASP B 465 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP B 122 " pdb=" OG1 THR B 473 " model vdw 2.354 3.040 nonbonded pdb=" OH TYR B 370 " pdb=" O TYR B 402 " model vdw 2.387 3.040 nonbonded pdb=" NH2 ARG B 127 " pdb=" O PHE B 234 " model vdw 2.389 3.120 ... (remaining 43100 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.290 Find NCS groups from input model: 0.020 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 : 0.006 0.160 5390 Z= 0.292 Angle : 1.032 55.064 7360 Z= 0.515 Chirality : 0.045 0.289 875 Planarity : 0.007 0.085 854 Dihedral : 12.741 102.984 2436 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.38 % Allowed : 1.89 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.31), residues: 624 helix: -1.14 (0.19), residues: 510 sheet: None (None), residues: 0 loop : 1.15 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG B 157 TYR 0.013 0.004 TYR B 315 PHE 0.017 0.002 PHE B 451 TRP 0.017 0.002 TRP B 215 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.29 ( 5390) covalent geometry : angle 1.03249 / 0.52 ( 7360) hydrogen bonds : bond 0.21300 / 13.67 ( 390) hydrogen bonds : angle 8.13121 / 6.04 ( 1158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.208 Fit side-chains REVERT: B 167 VAL cc_start: 0.8194 (t) cc_final: 0.7817 (m) REVERT: B 253 LYS cc_start: 0.8730 (mttt) cc_final: 0.8482 (mttp) REVERT: B 255 TYR cc_start: 0.7736 (m-80) cc_final: 0.7471 (p90) REVERT: B 269 LYS cc_start: 0.8225 (ttpp) cc_final: 0.8007 (ttpp) REVERT: B 288 ASN cc_start: 0.7950 (t0) cc_final: 0.7677 (t0) REVERT: B 318 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8366 (p-80) REVERT: B 328 LYS cc_start: 0.8224 (mttm) cc_final: 0.7967 (mtmp) REVERT: B 369 TYR cc_start: 0.7938 (t80) cc_final: 0.7695 (t80) REVERT: B 393 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7036 (tp40) REVERT: B 397 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 516 SER cc_start: 0.8911 (m) cc_final: 0.8574 (p) REVERT: B 533 LYS cc_start: 0.7575 (mtmt) cc_final: 0.6891 (mmtm) outliers start: 2 outliers final: 0 residues processed: 67 average time/residue: 0.5290 time to fit residues: 36.9672 Evaluate side-chains 50 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [54, 24, 48, 56, 26, 2, 16, 61, 32, 31, 25] chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN A 90 GLN B 243 ASN B 385 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095987 restraints weight = 6090.770| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.75 r_work: 0.2930 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5390 Z= 0.141 Angle : 0.543 6.156 7360 Z= 0.278 Chirality : 0.038 0.131 875 Planarity : 0.004 0.035 854 Dihedral : 8.683 61.881 1335 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.95 % Allowed : 5.68 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.34), residues: 624 helix: 1.39 (0.23), residues: 516 sheet: None (None), residues: 0 loop : 1.41 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.013 0.001 TYR B 428 PHE 0.013 0.001 PHE B 138 TRP 0.015 0.002 TRP B 215 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 5390) covalent geometry : angle 0.54289 / 0.28 ( 7360) hydrogen bonds : bond 0.05346 / 3.50 ( 390) hydrogen bonds : angle 4.35202 / 3.17 ( 1158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.201 Fit side-chains REVERT: A 33 ASP cc_start: 0.7964 (t0) cc_final: 0.7574 (t0) REVERT: B 183 GLU cc_start: 0.8577 (pt0) cc_final: 0.8362 (pt0) REVERT: B 253 LYS cc_start: 0.8834 (mttt) cc_final: 0.8504 (mttp) REVERT: B 255 TYR cc_start: 0.7774 (m-80) cc_final: 0.7296 (p90) REVERT: B 328 LYS cc_start: 0.7781 (mttm) cc_final: 0.7357 (mtmm) REVERT: B 369 TYR cc_start: 0.7905 (t80) cc_final: 0.7538 (t80) REVERT: B 495 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7626 (mmtm) REVERT: B 516 SER cc_start: 0.8612 (m) cc_final: 0.8215 (p) REVERT: B 533 LYS cc_start: 0.7026 (mtmt) cc_final: 0.6428 (mmtm) outliers start: 5 outliers final: 1 residues processed: 60 average time/residue: 0.5005 time to fit residues: 31.6002 Evaluate side-chains 51 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [46, 5, 34, 7, 9, 56, 10, 19, 1, 20, 8] chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 66 GLN B 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.094761 restraints weight = 6095.868| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.74 r_work: 0.2919 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5390 Z= 0.148 Angle : 0.521 6.218 7360 Z= 0.263 Chirality : 0.038 0.130 875 Planarity : 0.004 0.037 854 Dihedral : 8.411 60.456 1335 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.89 % Allowed : 6.44 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.34), residues: 624 helix: 2.03 (0.23), residues: 517 sheet: None (None), residues: 0 loop : 1.18 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 378 TYR 0.012 0.001 TYR B 428 PHE 0.012 0.001 PHE B 506 TRP 0.010 0.001 TRP B 215 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 5390) covalent geometry : angle 0.52055 / 0.26 ( 7360) hydrogen bonds : bond 0.05168 / 3.38 ( 390) hydrogen bonds : angle 4.12181 / 3.00 ( 1158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.167 Fit side-chains REVERT: A 33 ASP cc_start: 0.7948 (t0) cc_final: 0.7539 (t0) REVERT: B 123 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8166 (p) REVERT: B 124 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7651 (mm) REVERT: B 183 GLU cc_start: 0.8702 (pt0) cc_final: 0.8455 (pt0) REVERT: B 231 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7594 (mm) REVERT: B 253 LYS cc_start: 0.8897 (mttt) cc_final: 0.8569 (mttp) REVERT: B 255 TYR cc_start: 0.7892 (m-80) cc_final: 0.7352 (p90) REVERT: B 278 TYR cc_start: 0.7868 (m-80) cc_final: 0.7546 (m-80) REVERT: B 328 LYS cc_start: 0.7878 (mttm) cc_final: 0.7437 (mtmm) REVERT: B 369 TYR cc_start: 0.8006 (t80) cc_final: 0.7661 (t80) REVERT: B 495 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7742 (mmtm) REVERT: B 516 SER cc_start: 0.8757 (m) cc_final: 0.8334 (p) REVERT: B 533 LYS cc_start: 0.7190 (mtmt) cc_final: 0.6589 (mmtm) outliers start: 10 outliers final: 3 residues processed: 59 average time/residue: 0.4776 time to fit residues: 29.7435 Evaluate side-chains 53 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [52, 43, 25, 11, 24, 58, 39, 46, 34, 47, 27] chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 66 GLN B 288 ASN B 393 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094814 restraints weight = 6111.551| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.76 r_work: 0.2925 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5390 Z= 0.142 Angle : 0.502 5.654 7360 Z= 0.253 Chirality : 0.037 0.125 875 Planarity : 0.004 0.037 854 Dihedral : 8.270 60.084 1335 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.70 % Allowed : 7.20 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.35), residues: 624 helix: 2.27 (0.23), residues: 517 sheet: None (None), residues: 0 loop : 1.21 (0.63), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.012 0.001 TYR B 428 PHE 0.012 0.001 PHE B 506 TRP 0.008 0.001 TRP B 215 HIS 0.002 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 5390) covalent geometry : angle 0.50165 / 0.25 ( 7360) hydrogen bonds : bond 0.04904 / 3.20 ( 390) hydrogen bonds : angle 3.99811 / 2.91 ( 1158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.189 Fit side-chains REVERT: A 33 ASP cc_start: 0.7946 (t0) cc_final: 0.7521 (t0) REVERT: B 123 SER cc_start: 0.8513 (t) cc_final: 0.8214 (p) REVERT: B 124 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7706 (mm) REVERT: B 183 GLU cc_start: 0.8722 (pt0) cc_final: 0.8408 (pt0) REVERT: B 231 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7610 (mm) REVERT: B 253 LYS cc_start: 0.8910 (mttt) cc_final: 0.8582 (mttp) REVERT: B 255 TYR cc_start: 0.7936 (m-80) cc_final: 0.7375 (p90) REVERT: B 278 TYR cc_start: 0.7917 (m-80) cc_final: 0.7563 (m-80) REVERT: B 328 LYS cc_start: 0.7661 (mttm) cc_final: 0.7123 (mppt) REVERT: B 369 TYR cc_start: 0.7976 (t80) cc_final: 0.7639 (t80) REVERT: B 495 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7784 (mmtm) REVERT: B 516 SER cc_start: 0.8783 (m) cc_final: 0.8359 (p) REVERT: B 533 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6632 (mmtm) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.4569 time to fit residues: 27.0035 Evaluate side-chains 50 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [57, 45, 47, 31, 20, 50, 19, 36, 11, 51, 39] chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094653 restraints weight = 6185.805| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.77 r_work: 0.2902 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5390 Z= 0.138 Angle : 0.498 5.752 7360 Z= 0.249 Chirality : 0.037 0.120 875 Planarity : 0.004 0.037 854 Dihedral : 8.232 59.940 1335 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.70 % Allowed : 8.33 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.34), residues: 624 helix: 2.38 (0.23), residues: 516 sheet: None (None), residues: 0 loop : 1.19 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.011 0.001 TYR B 428 PHE 0.012 0.001 PHE B 506 TRP 0.007 0.001 TRP B 430 HIS 0.002 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5390) covalent geometry : angle 0.49770 / 0.25 ( 7360) hydrogen bonds : bond 0.04823 / 3.15 ( 390) hydrogen bonds : angle 3.94824 / 2.87 ( 1158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.194 Fit side-chains REVERT: A 33 ASP cc_start: 0.7911 (t0) cc_final: 0.7525 (t0) REVERT: B 123 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 124 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7689 (mm) REVERT: B 183 GLU cc_start: 0.8712 (pt0) cc_final: 0.8429 (pt0) REVERT: B 231 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7597 (mm) REVERT: B 253 LYS cc_start: 0.8911 (mttt) cc_final: 0.8567 (mttp) REVERT: B 255 TYR cc_start: 0.7947 (m-80) cc_final: 0.7368 (p90) REVERT: B 278 TYR cc_start: 0.7942 (m-80) cc_final: 0.7585 (m-80) REVERT: B 328 LYS cc_start: 0.7639 (mttm) cc_final: 0.7066 (mppt) REVERT: B 369 TYR cc_start: 0.7957 (t80) cc_final: 0.7629 (t80) REVERT: B 495 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7747 (mmtm) REVERT: B 516 SER cc_start: 0.8761 (m) cc_final: 0.8329 (p) REVERT: B 533 LYS cc_start: 0.7232 (mtmt) cc_final: 0.6638 (mmtm) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 0.4890 time to fit residues: 27.3468 Evaluate side-chains 51 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [42, 24, 30, 44, 55, 7, 37, 26, 18, 16, 3] chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 66 GLN B 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.096790 restraints weight = 6206.651| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.77 r_work: 0.2951 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5390 Z= 0.123 Angle : 0.476 5.170 7360 Z= 0.238 Chirality : 0.036 0.119 875 Planarity : 0.003 0.035 854 Dihedral : 8.082 59.146 1335 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.52 % Allowed : 8.52 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.35), residues: 624 helix: 2.46 (0.23), residues: 516 sheet: None (None), residues: 0 loop : 1.13 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.011 0.001 TYR B 428 PHE 0.010 0.001 PHE B 506 TRP 0.006 0.001 TRP B 430 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5390) covalent geometry : angle 0.47550 / 0.24 ( 7360) hydrogen bonds : bond 0.04499 / 2.94 ( 390) hydrogen bonds : angle 3.85143 / 2.79 ( 1158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.211 Fit side-chains REVERT: A 33 ASP cc_start: 0.7885 (t0) cc_final: 0.7424 (t0) REVERT: B 123 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 124 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7674 (mm) REVERT: B 183 GLU cc_start: 0.8701 (pt0) cc_final: 0.8398 (pt0) REVERT: B 253 LYS cc_start: 0.8896 (mttt) cc_final: 0.8546 (mttp) REVERT: B 255 TYR cc_start: 0.7932 (m-80) cc_final: 0.7345 (p90) REVERT: B 258 ARG cc_start: 0.8221 (mtt180) cc_final: 0.8015 (mtt90) REVERT: B 278 TYR cc_start: 0.7935 (m-80) cc_final: 0.7674 (m-80) REVERT: B 328 LYS cc_start: 0.7578 (mttm) cc_final: 0.7022 (mppt) REVERT: B 369 TYR cc_start: 0.7992 (t80) cc_final: 0.7665 (t80) REVERT: B 495 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7662 (tppt) REVERT: B 516 SER cc_start: 0.8843 (m) cc_final: 0.8408 (p) REVERT: B 533 LYS cc_start: 0.7215 (mtmt) cc_final: 0.6631 (mmtm) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.5172 time to fit residues: 32.5676 Evaluate side-chains 57 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [8, 42, 12, 18, 57, 44, 3, 10, 21, 20, 29] chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.094951 restraints weight = 6170.121| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.75 r_work: 0.2929 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5390 Z= 0.142 Angle : 0.494 5.089 7360 Z= 0.247 Chirality : 0.037 0.121 875 Planarity : 0.003 0.035 854 Dihedral : 8.181 59.957 1335 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.52 % Allowed : 9.66 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.35), residues: 624 helix: 2.43 (0.23), residues: 517 sheet: None (None), residues: 0 loop : 1.16 (0.63), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.011 0.001 TYR B 428 PHE 0.013 0.001 PHE B 506 TRP 0.007 0.001 TRP B 430 HIS 0.002 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 5390) covalent geometry : angle 0.49368 / 0.25 ( 7360) hydrogen bonds : bond 0.04761 / 3.11 ( 390) hydrogen bonds : angle 3.88538 / 2.81 ( 1158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.193 Fit side-chains REVERT: A 33 ASP cc_start: 0.7894 (t0) cc_final: 0.7477 (t0) REVERT: B 123 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8301 (p) REVERT: B 183 GLU cc_start: 0.8724 (pt0) cc_final: 0.8463 (pt0) REVERT: B 231 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7625 (mm) REVERT: B 253 LYS cc_start: 0.8893 (mttt) cc_final: 0.8541 (mttp) REVERT: B 255 TYR cc_start: 0.7946 (m-80) cc_final: 0.7344 (p90) REVERT: B 278 TYR cc_start: 0.7942 (m-80) cc_final: 0.7679 (m-80) REVERT: B 328 LYS cc_start: 0.7632 (mttm) cc_final: 0.7057 (mppt) REVERT: B 369 TYR cc_start: 0.7995 (t80) cc_final: 0.7667 (t80) REVERT: B 495 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7712 (mmtm) REVERT: B 516 SER cc_start: 0.8779 (m) cc_final: 0.8335 (p) REVERT: B 533 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6648 (mmtm) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.5023 time to fit residues: 27.5852 Evaluate side-chains 51 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [31, 46, 1, 48, 44, 57, 32, 6, 19, 37, 9] chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN A 115 HIS B 66 GLN B 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.094475 restraints weight = 6132.981| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.74 r_work: 0.2906 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5390 Z= 0.144 Angle : 0.499 5.087 7360 Z= 0.250 Chirality : 0.037 0.123 875 Planarity : 0.003 0.035 854 Dihedral : 8.209 60.536 1335 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.52 % Allowed : 9.47 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.34), residues: 624 helix: 2.42 (0.23), residues: 517 sheet: None (None), residues: 0 loop : 1.08 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.011 0.001 TYR B 428 PHE 0.013 0.001 PHE B 506 TRP 0.007 0.001 TRP B 430 HIS 0.002 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5390) covalent geometry : angle 0.49894 / 0.25 ( 7360) hydrogen bonds : bond 0.04837 / 3.16 ( 390) hydrogen bonds : angle 3.89723 / 2.82 ( 1158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.196 Fit side-chains REVERT: A 33 ASP cc_start: 0.7946 (t0) cc_final: 0.7529 (t0) REVERT: B 123 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 124 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7816 (mm) REVERT: B 183 GLU cc_start: 0.8779 (pt0) cc_final: 0.8537 (pt0) REVERT: B 231 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7759 (mm) REVERT: B 253 LYS cc_start: 0.8905 (mttt) cc_final: 0.8566 (mttp) REVERT: B 255 TYR cc_start: 0.7997 (m-80) cc_final: 0.7409 (p90) REVERT: B 278 TYR cc_start: 0.7966 (m-80) cc_final: 0.7709 (m-80) REVERT: B 328 LYS cc_start: 0.7754 (mttm) cc_final: 0.7172 (mppt) REVERT: B 369 TYR cc_start: 0.8087 (t80) cc_final: 0.7791 (t80) REVERT: B 495 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7857 (mmtm) REVERT: B 516 SER cc_start: 0.8838 (m) cc_final: 0.8422 (p) REVERT: B 533 LYS cc_start: 0.7387 (mtmt) cc_final: 0.6776 (mmtm) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.4685 time to fit residues: 25.7387 Evaluate side-chains 51 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [57, 58, 46, 35, 52, 37, 0, 50, 23, 49, 36] chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.095430 restraints weight = 6165.059| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.74 r_work: 0.2941 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5390 Z= 0.128 Angle : 0.483 5.017 7360 Z= 0.242 Chirality : 0.036 0.120 875 Planarity : 0.003 0.035 854 Dihedral : 8.131 59.961 1335 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.33 % Allowed : 9.66 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.34), residues: 624 helix: 2.48 (0.23), residues: 517 sheet: None (None), residues: 0 loop : 1.08 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 365 TYR 0.011 0.001 TYR B 428 PHE 0.012 0.001 PHE B 506 TRP 0.006 0.001 TRP B 430 HIS 0.002 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 5390) covalent geometry : angle 0.48283 / 0.24 ( 7360) hydrogen bonds : bond 0.04630 / 3.03 ( 390) hydrogen bonds : angle 3.84819 / 2.78 ( 1158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.159 Fit side-chains REVERT: A 33 ASP cc_start: 0.7930 (t0) cc_final: 0.7485 (t0) REVERT: B 123 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8252 (p) REVERT: B 124 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7712 (mm) REVERT: B 183 GLU cc_start: 0.8707 (pt0) cc_final: 0.8448 (pt0) REVERT: B 231 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7624 (mm) REVERT: B 253 LYS cc_start: 0.8914 (mttt) cc_final: 0.8559 (mttp) REVERT: B 255 TYR cc_start: 0.7949 (m-80) cc_final: 0.7379 (p90) REVERT: B 278 TYR cc_start: 0.7903 (m-80) cc_final: 0.7644 (m-80) REVERT: B 328 LYS cc_start: 0.7625 (mttm) cc_final: 0.7035 (mppt) REVERT: B 369 TYR cc_start: 0.8014 (t80) cc_final: 0.7703 (t80) REVERT: B 495 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7694 (tppt) REVERT: B 516 SER cc_start: 0.8774 (m) cc_final: 0.8349 (p) REVERT: B 533 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6658 (mmtm) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.4348 time to fit residues: 25.7736 Evaluate side-chains 60 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [31, 3, 20, 18, 59, 53, 12, 61, 33, 56, 14] chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.096714 restraints weight = 6083.971| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.74 r_work: 0.2954 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5390 Z= 0.125 Angle : 0.479 4.988 7360 Z= 0.241 Chirality : 0.036 0.119 875 Planarity : 0.003 0.035 854 Dihedral : 8.067 59.530 1335 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.95 % Allowed : 10.42 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.35), residues: 624 helix: 2.49 (0.23), residues: 517 sheet: None (None), residues: 0 loop : 1.05 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 365 TYR 0.011 0.001 TYR B 428 PHE 0.011 0.001 PHE B 506 TRP 0.007 0.001 TRP B 213 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 5390) covalent geometry : angle 0.47916 / 0.24 ( 7360) hydrogen bonds : bond 0.04534 / 2.96 ( 390) hydrogen bonds : angle 3.81804 / 2.77 ( 1158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.183 Fit side-chains REVERT: A 33 ASP cc_start: 0.7903 (t0) cc_final: 0.7460 (t0) REVERT: B 123 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 183 GLU cc_start: 0.8673 (pt0) cc_final: 0.8408 (pt0) REVERT: B 231 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7574 (mm) REVERT: B 253 LYS cc_start: 0.8910 (mttt) cc_final: 0.8555 (mttp) REVERT: B 255 TYR cc_start: 0.7946 (m-80) cc_final: 0.7379 (p90) REVERT: B 278 TYR cc_start: 0.7901 (m-80) cc_final: 0.7646 (m-80) REVERT: B 328 LYS cc_start: 0.7600 (mttm) cc_final: 0.7019 (mppt) REVERT: B 369 TYR cc_start: 0.8011 (t80) cc_final: 0.7703 (t80) REVERT: B 495 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7700 (tppt) REVERT: B 516 SER cc_start: 0.8829 (m) cc_final: 0.8408 (p) REVERT: B 533 LYS cc_start: 0.7241 (mtmt) cc_final: 0.6637 (mmtm) outliers start: 5 outliers final: 5 residues processed: 54 average time/residue: 0.5235 time to fit residues: 29.7374 Evaluate side-chains 55 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 318 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: [50, 58, 5, 6, 52, 53, 43, 55, 51, 30, 45] chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.095706 restraints weight = 6161.202| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.75 r_work: 0.2939 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5390 Z= 0.139 Angle : 0.493 5.023 7360 Z= 0.248 Chirality : 0.037 0.121 875 Planarity : 0.003 0.035 854 Dihedral : 8.119 59.947 1335 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.33 % Allowed : 10.23 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.34), residues: 624 helix: 2.43 (0.23), residues: 517 sheet: None (None), residues: 0 loop : 1.02 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.011 0.001 TYR B 428 PHE 0.013 0.001 PHE B 506 TRP 0.007 0.001 TRP B 430 HIS 0.002 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 5390) covalent geometry : angle 0.49253 / 0.25 ( 7360) hydrogen bonds : bond 0.04704 / 3.07 ( 390) hydrogen bonds : angle 3.85637 / 2.79 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.16 seconds wall clock time: 30 minutes 40.51 seconds (1840.51 seconds total)