Starting phenix.real_space_refine on Wed Jul 23 16:33:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7msx_23971/07_2025/7msx_23971.cif Found real_map, /net/cci-nas-00/data/ceres_data/7msx_23971/07_2025/7msx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7msx_23971/07_2025/7msx_23971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7msx_23971/07_2025/7msx_23971.map" model { file = "/net/cci-nas-00/data/ceres_data/7msx_23971/07_2025/7msx_23971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7msx_23971/07_2025/7msx_23971.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.01, per 1000 atoms: 0.81 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: 0.95 Conformation dependent library (CDL) restraints added in 453.6 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: 0.46 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: 1.11 Time building geometry restraints manager: 1.14 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: 1.370 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.930 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.003 TRP A 432 HIS 0.001 0.000 HIS A 56 PHE 0.010 0.001 PHE A 93 TYR 0.013 0.001 TYR A 207 ARG 0.002 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.19270 ( 170) hydrogen bonds : angle 7.02227 ( 492) metal coordination : bond 0.20926 ( 12) metal coordination : angle 21.27377 ( 10) covalent geometry : bond 0.00803 ( 3777) covalent geometry : angle 0.62196 ( 5103) *********************** 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 : 0.403 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: 0.2146 time to fit residues: 25.5162 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 : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097783 restraints weight = 4846.721| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.14 r_work: 0.3043 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3789 Z= 0.125 Angle : 0.558 11.451 5113 Z= 0.277 Chirality : 0.040 0.151 573 Planarity : 0.004 0.024 649 Dihedral : 4.313 20.492 502 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.21 % Allowed : 4.91 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.38), residues: 467 helix: 1.84 (0.36), residues: 180 sheet: -0.65 (0.53), residues: 74 loop : 0.40 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 432 HIS 0.003 0.001 HIS A 194 PHE 0.011 0.001 PHE A 41 TYR 0.015 0.001 TYR A 207 ARG 0.005 0.001 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 170) hydrogen bonds : angle 4.73258 ( 492) metal coordination : bond 0.02041 ( 12) metal coordination : angle 5.78116 ( 10) covalent geometry : bond 0.00281 ( 3777) covalent geometry : angle 0.49682 ( 5103) *********************** 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 : 0.444 Fit side-chains REVERT: A 264 GLU cc_start: 0.8016 (pm20) cc_final: 0.7689 (mp0) REVERT: A 383 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: A 428 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8463 (tt) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.2213 time to fit residues: 16.1118 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 : 0.423 ------------------------------------------------------------------------------- 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 36 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.093807 restraints weight = 4838.733| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.14 r_work: 0.2977 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3789 Z= 0.183 Angle : 0.581 12.862 5113 Z= 0.290 Chirality : 0.042 0.196 573 Planarity : 0.004 0.028 649 Dihedral : 4.390 20.975 502 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.21 % Allowed : 6.63 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.38), residues: 467 helix: 1.97 (0.37), residues: 180 sheet: -0.88 (0.53), residues: 74 loop : 0.08 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 432 HIS 0.004 0.001 HIS A 194 PHE 0.012 0.001 PHE A 41 TYR 0.016 0.002 TYR A 207 ARG 0.005 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 170) hydrogen bonds : angle 4.70032 ( 492) metal coordination : bond 0.01505 ( 12) metal coordination : angle 5.51278 ( 10) covalent geometry : bond 0.00444 ( 3777) covalent geometry : angle 0.52766 ( 5103) *********************** 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: 9 poor density : 44 time to evaluate : 0.401 Fit side-chains REVERT: A 268 ASP cc_start: 0.7984 (m-30) cc_final: 0.7782 (m-30) REVERT: A 383 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: A 428 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8505 (tt) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1865 time to fit residues: 11.4805 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 : 0.440 ------------------------------------------------------------------------------- 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 104 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 0.0010 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.129996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098457 restraints weight = 4871.867| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.17 r_work: 0.3046 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3789 Z= 0.090 Angle : 0.473 10.302 5113 Z= 0.238 Chirality : 0.038 0.164 573 Planarity : 0.003 0.029 649 Dihedral : 3.969 16.793 502 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.97 % Allowed : 6.63 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.38), residues: 467 helix: 1.99 (0.38), residues: 182 sheet: -0.87 (0.53), residues: 74 loop : 0.20 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 432 HIS 0.002 0.000 HIS A 194 PHE 0.009 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.005 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 170) hydrogen bonds : angle 4.36102 ( 492) metal coordination : bond 0.00747 ( 12) metal coordination : angle 4.21838 ( 10) covalent geometry : bond 0.00202 ( 3777) covalent geometry : angle 0.43503 ( 5103) *********************** 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 50 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.450 Fit side-chains REVERT: A 55 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6219 (pp20) REVERT: A 383 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7973 (tt0) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.1879 time to fit residues: 10.9979 Evaluate side-chains 46 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 383 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.128248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096596 restraints weight = 4951.474| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.16 r_work: 0.3017 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3789 Z= 0.114 Angle : 0.473 10.259 5113 Z= 0.242 Chirality : 0.039 0.163 573 Planarity : 0.003 0.030 649 Dihedral : 3.942 18.265 502 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.70 % Allowed : 6.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.38), residues: 467 helix: 2.08 (0.38), residues: 180 sheet: -0.77 (0.54), residues: 74 loop : 0.15 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 432 HIS 0.003 0.001 HIS A 194 PHE 0.006 0.001 PHE A 471 TYR 0.013 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 170) hydrogen bonds : angle 4.28317 ( 492) metal coordination : bond 0.00821 ( 12) metal coordination : angle 4.24177 ( 10) covalent geometry : bond 0.00272 ( 3777) covalent geometry : angle 0.43416 ( 5103) *********************** 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: 11 poor density : 42 time to evaluate : 0.403 Fit side-chains REVERT: A 55 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6253 (pp20) REVERT: A 383 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8034 (tt0) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 0.1934 time to fit residues: 11.2478 Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 0.0030 chunk 8 optimal weight: 0.0170 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.0170 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 overall best weight: 0.0724 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.133662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102985 restraints weight = 4875.163| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.12 r_work: 0.3127 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3789 Z= 0.077 Angle : 0.433 7.994 5113 Z= 0.222 Chirality : 0.037 0.149 573 Planarity : 0.003 0.030 649 Dihedral : 3.553 13.265 502 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.47 % Allowed : 8.60 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.38), residues: 467 helix: 1.81 (0.38), residues: 190 sheet: -0.66 (0.54), residues: 74 loop : 0.32 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 432 HIS 0.001 0.000 HIS A 194 PHE 0.007 0.001 PHE A 41 TYR 0.011 0.001 TYR A 207 ARG 0.004 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.02624 ( 170) hydrogen bonds : angle 3.97899 ( 492) metal coordination : bond 0.00602 ( 12) metal coordination : angle 3.08890 ( 10) covalent geometry : bond 0.00161 ( 3777) covalent geometry : angle 0.41138 ( 5103) *********************** 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 61 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.444 Fit side-chains REVERT: A 23 ASP cc_start: 0.8181 (t70) cc_final: 0.7909 (t0) REVERT: A 55 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6237 (pp20) outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 0.1645 time to fit residues: 11.6273 Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.127098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.095631 restraints weight = 4889.627| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.11 r_work: 0.3006 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3789 Z= 0.148 Angle : 0.529 10.423 5113 Z= 0.266 Chirality : 0.040 0.162 573 Planarity : 0.003 0.032 649 Dihedral : 3.926 18.797 502 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.72 % Allowed : 9.58 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.38), residues: 467 helix: 2.05 (0.38), residues: 182 sheet: -0.73 (0.56), residues: 74 loop : 0.13 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 54 PHE 0.015 0.001 PHE A 287 TYR 0.012 0.001 TYR A 207 ARG 0.005 0.001 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 170) hydrogen bonds : angle 4.22417 ( 492) metal coordination : bond 0.00946 ( 12) metal coordination : angle 4.48430 ( 10) covalent geometry : bond 0.00357 ( 3777) covalent geometry : angle 0.49044 ( 5103) *********************** 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 50 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 1.023 Fit side-chains REVERT: A 23 ASP cc_start: 0.8286 (t70) cc_final: 0.8042 (t0) REVERT: A 55 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6267 (pp20) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.1905 time to fit residues: 11.5810 Evaluate side-chains 45 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 126 VAL 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 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.128992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097411 restraints weight = 4925.380| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.14 r_work: 0.3040 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3789 Z= 0.101 Angle : 0.481 9.020 5113 Z= 0.244 Chirality : 0.039 0.157 573 Planarity : 0.003 0.031 649 Dihedral : 3.753 16.534 502 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.47 % Allowed : 10.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.38), residues: 467 helix: 2.07 (0.38), residues: 182 sheet: -0.68 (0.57), residues: 74 loop : 0.15 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.022 0.001 PHE A 41 TYR 0.012 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 170) hydrogen bonds : angle 4.14253 ( 492) metal coordination : bond 0.00707 ( 12) metal coordination : angle 3.68360 ( 10) covalent geometry : bond 0.00236 ( 3777) covalent geometry : angle 0.45337 ( 5103) *********************** 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 52 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.538 Fit side-chains REVERT: A 55 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6223 (pp20) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.2851 time to fit residues: 18.3228 Evaluate side-chains 45 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.129551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099507 restraints weight = 4792.335| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.02 r_work: 0.3062 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4275 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= 0.094 Angle : 0.474 9.136 5113 Z= 0.241 Chirality : 0.039 0.155 573 Planarity : 0.003 0.031 649 Dihedral : 3.679 15.889 502 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.23 % Allowed : 11.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.39), residues: 467 helix: 1.89 (0.38), residues: 189 sheet: -0.70 (0.57), residues: 74 loop : 0.25 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.001 0.000 HIS A 194 PHE 0.023 0.001 PHE A 41 TYR 0.011 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 170) hydrogen bonds : angle 4.06672 ( 492) metal coordination : bond 0.00652 ( 12) metal coordination : angle 3.39712 ( 10) covalent geometry : bond 0.00219 ( 3777) covalent geometry : angle 0.44962 ( 5103) *********************** 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 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.512 Fit side-chains REVERT: A 55 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6113 (pp20) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.3302 time to fit residues: 18.4904 Evaluate side-chains 43 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.095615 restraints weight = 4855.614| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.09 r_work: 0.3006 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4212 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= 0.133 Angle : 0.527 10.119 5113 Z= 0.265 Chirality : 0.040 0.162 573 Planarity : 0.003 0.032 649 Dihedral : 3.924 18.853 502 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.23 % Allowed : 11.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.38), residues: 467 helix: 1.86 (0.38), residues: 188 sheet: -0.61 (0.58), residues: 72 loop : 0.19 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.002 0.001 HIS A 54 PHE 0.023 0.001 PHE A 41 TYR 0.011 0.001 TYR A 207 ARG 0.005 0.001 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 170) hydrogen bonds : angle 4.22815 ( 492) metal coordination : bond 0.00829 ( 12) metal coordination : angle 4.07024 ( 10) covalent geometry : bond 0.00324 ( 3777) covalent geometry : angle 0.49628 ( 5103) ********************** 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 43 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.655 Fit side-chains REVERT: A 55 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6123 (pp20) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.3553 time to fit residues: 17.7057 Evaluate side-chains 42 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 126 VAL 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 24 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.127717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096173 restraints weight = 4897.369| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.11 r_work: 0.3017 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3789 Z= 0.122 Angle : 0.510 9.783 5113 Z= 0.257 Chirality : 0.039 0.161 573 Planarity : 0.004 0.032 649 Dihedral : 3.881 18.151 502 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.47 % Allowed : 11.30 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.38), residues: 467 helix: 1.95 (0.38), residues: 183 sheet: -0.68 (0.59), residues: 72 loop : 0.09 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.002 0.001 HIS A 54 PHE 0.024 0.001 PHE A 41 TYR 0.012 0.001 TYR A 207 ARG 0.006 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 170) hydrogen bonds : angle 4.23333 ( 492) metal coordination : bond 0.00819 ( 12) metal coordination : angle 3.86039 ( 10) covalent geometry : bond 0.00293 ( 3777) covalent geometry : angle 0.48076 ( 5103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2883.91 seconds wall clock time: 52 minutes 30.17 seconds (3150.17 seconds total)