Starting phenix.real_space_refine on Tue Mar 3 12:00:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7msx_23971/03_2026/7msx_23971.cif Found real_map, /net/cci-nas-00/data/ceres_data/7msx_23971/03_2026/7msx_23971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7msx_23971/03_2026/7msx_23971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7msx_23971/03_2026/7msx_23971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7msx_23971/03_2026/7msx_23971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7msx_23971/03_2026/7msx_23971.map" } resolution = 3.15 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= 0.003 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 Zn 3 6.06 5 S 26 5.16 5 C 2359 2.51 5 N 620 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3706 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3703 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1016 SG CYS A 143 13.882 35.673 58.737 1.00 38.05 S ATOM 1040 SG CYS A 146 12.818 36.968 62.628 1.00 47.40 S ATOM 1153 SG CYS A 161 16.687 37.445 59.660 1.00 42.84 S ATOM 1179 SG CYS A 164 15.449 34.581 62.038 1.00 44.32 S ATOM 1371 SG CYS A 190 28.609 18.258 44.496 1.00 54.40 S ATOM 1389 SG CYS A 193 30.905 15.408 45.275 1.00 70.39 S ATOM 1713 SG CYS A 236 31.982 19.316 43.189 1.00 52.65 S ATOM 136 SG CYS A 20 17.151 42.649 18.557 1.00 45.24 S ATOM 372 SG CYS A 51 16.203 45.352 15.948 1.00 45.63 S Time building chain proxies: 0.82, per 1000 atoms: 0.22 Number of scatterers: 3706 At special positions: 0 Unit cell: (57.546, 75.894, 114.258, 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) Zn 3 29.99 S 26 16.00 O 698 8.00 N 620 7.00 C 2359 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: 0.28 Conformation dependent library (CDL) restraints added in 135.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 143 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 164 " pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 202 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 190 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 193 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 56 " pdb="ZN ZN A 703 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 20 " Number of angles added : 10 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 46.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 203 through 212 removed outlier: 4.250A pdb=" N GLY A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.562A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.732A pdb=" N LYS A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 378 through 394 Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.671A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 492 through 503 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.456A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA A 184 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN A 133 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 187 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.456A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 235 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 244 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 233 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG A 246 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 231 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A 248 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N CYS A 229 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR A 233 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG A 222 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.678A pdb=" N LEU A 137 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 334 removed outlier: 6.106A pdb=" N VAL A 279 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A 332 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 281 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY A 334 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 283 " --> pdb=" O GLY A 334 " (cutoff:3.500A) 181 hydrogen bonds defined for protein. 492 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: 0.57 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 722 1.33 - 1.45: 924 1.45 - 1.57: 2100 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3777 Sorted by residual: bond pdb=" N PRO A 91 " pdb=" CD PRO A 91 " ideal model delta sigma weight residual 1.473 1.400 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" N PRO A 200 " pdb=" CD PRO A 200 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" N PRO A 13 " pdb=" CD PRO A 13 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" N PRO A 17 " pdb=" CD PRO A 17 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 1.473 1.417 0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 3772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4853 1.27 - 2.53: 203 2.53 - 3.80: 43 3.80 - 5.06: 1 5.06 - 6.33: 3 Bond angle restraints: 5103 Sorted by residual: angle pdb=" N GLY A 327 " pdb=" CA GLY A 327 " pdb=" C GLY A 327 " ideal model delta sigma weight residual 115.21 121.46 -6.25 1.30e+00 5.92e-01 2.31e+01 angle pdb=" C ALA A 26 " pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 120.28 116.58 3.70 1.34e+00 5.57e-01 7.63e+00 angle pdb=" CA TRP A 432 " pdb=" CB TRP A 432 " pdb=" CG TRP A 432 " ideal model delta sigma weight residual 113.60 118.78 -5.18 1.90e+00 2.77e-01 7.44e+00 angle pdb=" C VAL A 234 " pdb=" CA VAL A 234 " pdb=" CB VAL A 234 " ideal model delta sigma weight residual 111.44 109.09 2.35 9.50e-01 1.11e+00 6.11e+00 angle pdb=" C VAL A 157 " pdb=" CA VAL A 157 " pdb=" CB VAL A 157 " ideal model delta sigma weight residual 111.44 109.29 2.15 9.50e-01 1.11e+00 5.14e+00 ... (remaining 5098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 2119 14.59 - 29.17: 99 29.17 - 43.76: 21 43.76 - 58.34: 7 58.34 - 72.92: 3 Dihedral angle restraints: 2249 sinusoidal: 885 harmonic: 1364 Sorted by residual: dihedral pdb=" CA GLY A 344 " pdb=" C GLY A 344 " pdb=" N GLU A 345 " pdb=" CA GLU A 345 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA SER A 351 " pdb=" C SER A 351 " pdb=" N PRO A 352 " pdb=" CA PRO A 352 " ideal model delta harmonic sigma weight residual 180.00 165.40 14.60 0 5.00e+00 4.00e-02 8.53e+00 dihedral pdb=" CA PHE A 329 " pdb=" C PHE A 329 " pdb=" N LYS A 330 " pdb=" CA LYS A 330 " ideal model delta harmonic sigma weight residual 180.00 165.44 14.56 0 5.00e+00 4.00e-02 8.48e+00 ... (remaining 2246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 375 0.033 - 0.067: 91 0.067 - 0.100: 56 0.100 - 0.134: 36 0.134 - 0.167: 15 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA VAL A 186 " pdb=" N VAL A 186 " pdb=" C VAL A 186 " pdb=" CB VAL A 186 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA VAL A 230 " pdb=" N VAL A 230 " pdb=" C VAL A 230 " pdb=" CB VAL A 230 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 570 not shown) Planarity restraints: 649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.016 2.00e-02 2.50e+03 1.30e-02 4.20e+00 pdb=" CG TRP A 432 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 464 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C ASP A 464 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 464 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 465 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 463 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ARG A 463 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG A 463 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 464 " -0.008 2.00e-02 2.50e+03 ... (remaining 646 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1457 2.89 - 3.39: 3529 3.39 - 3.89: 6079 3.89 - 4.40: 7034 4.40 - 4.90: 11643 Nonbonded interactions: 29742 Sorted by model distance: nonbonded pdb=" O GLU A 272 " pdb=" NZ LYS A 276 " model vdw 2.385 3.120 nonbonded pdb=" NZ LYS A 288 " pdb=" OD2 ASP A 409 " model vdw 2.388 3.120 nonbonded pdb=" OD2 ASP A 23 " pdb=" NH1 ARG A 27 " model vdw 2.476 3.120 nonbonded pdb=" NZ LYS A 320 " pdb=" OE2 GLU A 324 " model vdw 2.561 3.120 nonbonded pdb=" N GLU A 373 " pdb=" OE1 GLU A 373 " model vdw 2.566 3.120 ... (remaining 29737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.430 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.014 0.341 3789 Z= 0.592 Angle : 1.127 44.267 5113 Z= 0.440 Chirality : 0.052 0.167 573 Planarity : 0.003 0.023 649 Dihedral : 10.301 72.925 1371 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.36), residues: 467 helix: 0.34 (0.34), residues: 180 sheet: -0.85 (0.52), residues: 74 loop : 0.34 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 463 TYR 0.013 0.001 TYR A 207 PHE 0.010 0.001 PHE A 93 TRP 0.036 0.003 TRP A 432 HIS 0.001 0.000 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00803 ( 3777) covalent geometry : angle 0.62196 ( 5103) hydrogen bonds : bond 0.19270 ( 170) hydrogen bonds : angle 7.02227 ( 492) metal coordination : bond 0.20926 ( 12) metal coordination : angle 21.27377 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8541 (pttt) cc_final: 0.8334 (pttm) REVERT: A 499 PHE cc_start: 0.7890 (t80) cc_final: 0.7633 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0929 time to fit residues: 11.1465 Evaluate side-chains 58 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 152 GLN A 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097763 restraints weight = 4884.409| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.11 r_work: 0.3042 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3789 Z= 0.127 Angle : 0.561 11.158 5113 Z= 0.280 Chirality : 0.040 0.152 573 Planarity : 0.004 0.023 649 Dihedral : 4.328 20.592 502 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.21 % Allowed : 5.16 % Favored : 92.63 % 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: 1.08 (0.38), residues: 467 helix: 1.83 (0.36), residues: 180 sheet: -0.67 (0.53), residues: 74 loop : 0.41 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 246 TYR 0.016 0.001 TYR A 207 PHE 0.010 0.001 PHE A 41 TRP 0.023 0.002 TRP A 432 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3777) covalent geometry : angle 0.50248 ( 5103) hydrogen bonds : bond 0.04150 ( 170) hydrogen bonds : angle 4.73449 ( 492) metal coordination : bond 0.01816 ( 12) metal coordination : angle 5.63863 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.141 Fit side-chains REVERT: A 264 GLU cc_start: 0.8010 (pm20) cc_final: 0.7701 (mp0) REVERT: A 383 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: A 428 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8463 (tt) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.0943 time to fit residues: 6.7610 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098215 restraints weight = 4788.419| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.11 r_work: 0.3053 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3789 Z= 0.105 Angle : 0.493 10.564 5113 Z= 0.249 Chirality : 0.039 0.173 573 Planarity : 0.003 0.026 649 Dihedral : 4.017 17.239 502 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.97 % Allowed : 7.13 % Favored : 90.91 % 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: 1.14 (0.38), residues: 467 helix: 2.04 (0.38), residues: 182 sheet: -0.69 (0.53), residues: 74 loop : 0.28 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 46 TYR 0.013 0.001 TYR A 207 PHE 0.013 0.001 PHE A 41 TRP 0.018 0.001 TRP A 432 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3777) covalent geometry : angle 0.45240 ( 5103) hydrogen bonds : bond 0.03529 ( 170) hydrogen bonds : angle 4.43458 ( 492) metal coordination : bond 0.01292 ( 12) metal coordination : angle 4.46316 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.147 Fit side-chains REVERT: A 79 LEU cc_start: 0.8842 (tp) cc_final: 0.8638 (tp) REVERT: A 218 ARG cc_start: 0.6872 (mmm160) cc_final: 0.6579 (mmm160) REVERT: A 383 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: A 428 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8498 (tt) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.0773 time to fit residues: 4.7542 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098653 restraints weight = 4803.372| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.03 r_work: 0.3043 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3789 Z= 0.114 Angle : 0.488 10.423 5113 Z= 0.247 Chirality : 0.039 0.168 573 Planarity : 0.003 0.029 649 Dihedral : 3.997 18.405 502 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.21 % Allowed : 6.14 % Favored : 91.65 % 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: 1.08 (0.38), residues: 467 helix: 2.09 (0.37), residues: 180 sheet: -0.82 (0.53), residues: 74 loop : 0.20 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 46 TYR 0.013 0.001 TYR A 207 PHE 0.009 0.001 PHE A 41 TRP 0.025 0.002 TRP A 432 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3777) covalent geometry : angle 0.44878 ( 5103) hydrogen bonds : bond 0.03515 ( 170) hydrogen bonds : angle 4.39881 ( 492) metal coordination : bond 0.00834 ( 12) metal coordination : angle 4.35682 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.097 Fit side-chains REVERT: A 55 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6309 (pp20) REVERT: A 383 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7976 (tt0) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.0929 time to fit residues: 5.5110 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096175 restraints weight = 4817.423| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.13 r_work: 0.3016 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3789 Z= 0.120 Angle : 0.493 10.710 5113 Z= 0.247 Chirality : 0.039 0.164 573 Planarity : 0.003 0.030 649 Dihedral : 3.987 19.114 502 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.21 % Allowed : 7.13 % Favored : 90.66 % 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: 1.08 (0.38), residues: 467 helix: 2.03 (0.38), residues: 182 sheet: -0.75 (0.54), residues: 74 loop : 0.21 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 222 TYR 0.013 0.001 TYR A 207 PHE 0.008 0.001 PHE A 41 TRP 0.013 0.001 TRP A 432 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3777) covalent geometry : angle 0.45249 ( 5103) hydrogen bonds : bond 0.03429 ( 170) hydrogen bonds : angle 4.26955 ( 492) metal coordination : bond 0.00843 ( 12) metal coordination : angle 4.47200 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.123 Fit side-chains REVERT: A 55 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6213 (pp20) REVERT: A 383 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8068 (tt0) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.0825 time to fit residues: 4.7759 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 3 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096932 restraints weight = 4841.094| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.04 r_work: 0.3014 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3789 Z= 0.124 Angle : 0.477 10.280 5113 Z= 0.243 Chirality : 0.039 0.160 573 Planarity : 0.003 0.030 649 Dihedral : 3.981 18.976 502 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.46 % Allowed : 8.11 % Favored : 89.43 % 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: 1.05 (0.38), residues: 467 helix: 1.90 (0.37), residues: 186 sheet: -0.69 (0.55), residues: 74 loop : 0.24 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 TYR 0.013 0.001 TYR A 207 PHE 0.018 0.001 PHE A 41 TRP 0.011 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3777) covalent geometry : angle 0.43724 ( 5103) hydrogen bonds : bond 0.03454 ( 170) hydrogen bonds : angle 4.26778 ( 492) metal coordination : bond 0.00859 ( 12) metal coordination : angle 4.35707 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.136 Fit side-chains REVERT: A 55 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6220 (pp20) REVERT: A 383 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8066 (tt0) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.0774 time to fit residues: 4.1439 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.0040 chunk 42 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097526 restraints weight = 4917.199| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.14 r_work: 0.3040 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3789 Z= 0.095 Angle : 0.465 9.326 5113 Z= 0.233 Chirality : 0.038 0.156 573 Planarity : 0.003 0.030 649 Dihedral : 3.835 17.211 502 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.46 % Allowed : 8.35 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.38), residues: 467 helix: 1.97 (0.38), residues: 186 sheet: -0.69 (0.55), residues: 74 loop : 0.27 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 TYR 0.012 0.001 TYR A 207 PHE 0.016 0.001 PHE A 41 TRP 0.010 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 3777) covalent geometry : angle 0.43291 ( 5103) hydrogen bonds : bond 0.03077 ( 170) hydrogen bonds : angle 4.14835 ( 492) metal coordination : bond 0.00755 ( 12) metal coordination : angle 3.83407 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.183 Fit side-chains REVERT: A 23 ASP cc_start: 0.8279 (t70) cc_final: 0.7910 (t0) REVERT: A 27 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8186 (mtt90) REVERT: A 55 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6228 (pp20) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.0760 time to fit residues: 4.8336 Evaluate side-chains 50 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095881 restraints weight = 4873.336| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.11 r_work: 0.3015 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3789 Z= 0.125 Angle : 0.500 9.894 5113 Z= 0.250 Chirality : 0.039 0.159 573 Planarity : 0.003 0.031 649 Dihedral : 3.972 18.837 502 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.97 % Allowed : 9.58 % 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: 1.05 (0.38), residues: 467 helix: 1.86 (0.38), residues: 188 sheet: -0.72 (0.56), residues: 74 loop : 0.27 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 222 TYR 0.012 0.001 TYR A 207 PHE 0.022 0.001 PHE A 41 TRP 0.008 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3777) covalent geometry : angle 0.46401 ( 5103) hydrogen bonds : bond 0.03393 ( 170) hydrogen bonds : angle 4.25238 ( 492) metal coordination : bond 0.00874 ( 12) metal coordination : angle 4.25883 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.170 Fit side-chains REVERT: A 55 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6189 (pp20) outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 0.0859 time to fit residues: 4.9090 Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.0070 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097102 restraints weight = 4881.364| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.12 r_work: 0.3031 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3789 Z= 0.112 Angle : 0.499 9.702 5113 Z= 0.249 Chirality : 0.039 0.157 573 Planarity : 0.003 0.031 649 Dihedral : 3.891 17.987 502 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.97 % Allowed : 10.07 % Favored : 87.96 % 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: 1.09 (0.38), residues: 467 helix: 2.05 (0.38), residues: 182 sheet: -0.73 (0.56), residues: 74 loop : 0.21 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 222 TYR 0.012 0.001 TYR A 207 PHE 0.022 0.001 PHE A 41 TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3777) covalent geometry : angle 0.46587 ( 5103) hydrogen bonds : bond 0.03208 ( 170) hydrogen bonds : angle 4.21303 ( 492) metal coordination : bond 0.00872 ( 12) metal coordination : angle 4.08951 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.193 Fit side-chains REVERT: A 55 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6174 (pp20) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.0877 time to fit residues: 4.7987 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097556 restraints weight = 4931.408| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.12 r_work: 0.3040 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3789 Z= 0.106 Angle : 0.498 9.324 5113 Z= 0.250 Chirality : 0.039 0.155 573 Planarity : 0.003 0.032 649 Dihedral : 3.841 17.401 502 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.97 % Allowed : 10.32 % Favored : 87.71 % 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: 1.09 (0.38), residues: 467 helix: 2.05 (0.38), residues: 182 sheet: -0.73 (0.56), residues: 74 loop : 0.21 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 27 TYR 0.012 0.001 TYR A 207 PHE 0.021 0.001 PHE A 41 TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3777) covalent geometry : angle 0.46796 ( 5103) hydrogen bonds : bond 0.03050 ( 170) hydrogen bonds : angle 4.14685 ( 492) metal coordination : bond 0.00815 ( 12) metal coordination : angle 3.90925 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.106 Fit side-chains REVERT: A 55 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6173 (pp20) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.0705 time to fit residues: 3.9505 Evaluate side-chains 47 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.0000 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097034 restraints weight = 4855.558| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.12 r_work: 0.3030 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3789 Z= 0.110 Angle : 0.504 9.132 5113 Z= 0.252 Chirality : 0.039 0.156 573 Planarity : 0.003 0.031 649 Dihedral : 3.846 17.873 502 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.97 % Allowed : 10.57 % Favored : 87.47 % 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: 1.05 (0.38), residues: 467 helix: 2.02 (0.38), residues: 182 sheet: -0.79 (0.57), residues: 74 loop : 0.20 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 27 TYR 0.012 0.001 TYR A 207 PHE 0.021 0.001 PHE A 41 TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3777) covalent geometry : angle 0.47437 ( 5103) hydrogen bonds : bond 0.03105 ( 170) hydrogen bonds : angle 4.16467 ( 492) metal coordination : bond 0.00845 ( 12) metal coordination : angle 3.85757 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1213.29 seconds wall clock time: 21 minutes 23.37 seconds (1283.37 seconds total)