Starting phenix.real_space_refine on Fri Aug 22 14:28:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3s_27871/08_2025/8e3s_27871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3s_27871/08_2025/8e3s_27871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e3s_27871/08_2025/8e3s_27871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3s_27871/08_2025/8e3s_27871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e3s_27871/08_2025/8e3s_27871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3s_27871/08_2025/8e3s_27871.map" } resolution = 3.1 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= 0.011 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 1 6.06 5 S 32 5.16 5 C 2610 2.51 5 N 672 2.21 5 O 757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4072 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4071 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 477} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 158 SG CYS A 20 22.552 25.108 49.930 1.00201.97 S ATOM 180 SG CYS A 23 22.465 22.074 49.200 1.00201.28 S ATOM 754 SG CYS A 94 23.485 21.317 52.197 1.00184.63 S ATOM 760 SG CYS A 95 25.414 23.447 49.428 1.00177.00 S Time building chain proxies: 1.01, per 1000 atoms: 0.25 Number of scatterers: 4072 At special positions: 0 Unit cell: (68.9354, 73.2984, 95.986, 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 1 29.99 S 32 16.00 O 757 8.00 N 672 7.00 C 2610 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: 0.36 Conformation dependent library (CDL) restraints added in 156.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 23 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 95 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 20 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 94 " Number of angles added : 6 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 43.7% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.826A pdb=" N LEU A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 35 " --> pdb=" O MET A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 35' Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.667A pdb=" N LEU A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 138 through 149 removed outlier: 3.724A pdb=" N ASN A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.894A pdb=" N TYR A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.695A pdb=" N MET A 218 " --> pdb=" O TRP A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.620A pdb=" N SER A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 268 through 284 removed outlier: 3.596A pdb=" N LEU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 353 through 357 removed outlier: 3.763A pdb=" N ARG A 357 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.838A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.756A pdb=" N GLY A 59 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 86 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 79 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.756A pdb=" N GLY A 59 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 62 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP A 8 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A 5 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 498 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE A 7 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 454 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 294 removed outlier: 5.325A pdb=" N TYR A 290 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR A 102 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY A 292 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR A 99 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 101 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 320 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 318 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 158 removed outlier: 3.657A pdb=" N TYR A 154 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 242 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR A 236 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE A 241 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TRP A 260 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE A 243 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE A 258 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL A 245 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 256 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 247 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 254 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338 166 hydrogen bonds defined for protein. 426 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: 1.10 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1301 1.34 - 1.46: 968 1.46 - 1.58: 1857 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 4175 Sorted by residual: bond pdb=" CG GLU A 389 " pdb=" CD GLU A 389 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CD GLU A 389 " pdb=" OE1 GLU A 389 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.04e-01 bond pdb=" C PHE A 361 " pdb=" O PHE A 361 " ideal model delta sigma weight residual 1.248 1.238 0.010 1.26e-02 6.30e+03 6.68e-01 bond pdb=" N GLU A 389 " pdb=" CA GLU A 389 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.28e-02 6.10e+03 5.08e-01 bond pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " ideal model delta sigma weight residual 1.528 1.540 -0.011 1.66e-02 3.63e+03 4.78e-01 ... (remaining 4170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 5484 1.46 - 2.91: 125 2.91 - 4.37: 26 4.37 - 5.82: 6 5.82 - 7.28: 3 Bond angle restraints: 5644 Sorted by residual: angle pdb=" N GLU A 389 " pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " ideal model delta sigma weight residual 110.28 115.74 -5.46 1.55e+00 4.16e-01 1.24e+01 angle pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " pdb=" CG GLU A 389 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.45e+00 angle pdb=" C ASN A 388 " pdb=" N GLU A 389 " pdb=" CA GLU A 389 " ideal model delta sigma weight residual 120.31 116.34 3.97 1.52e+00 4.33e-01 6.84e+00 angle pdb=" N ARG A 79 " pdb=" CA ARG A 79 " pdb=" CB ARG A 79 " ideal model delta sigma weight residual 111.00 115.49 -4.49 1.81e+00 3.05e-01 6.15e+00 angle pdb=" N LYS A 27 " pdb=" CA LYS A 27 " pdb=" C LYS A 27 " ideal model delta sigma weight residual 114.09 110.27 3.82 1.55e+00 4.16e-01 6.06e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2265 17.84 - 35.68: 210 35.68 - 53.52: 25 53.52 - 71.36: 5 71.36 - 89.20: 2 Dihedral angle restraints: 2507 sinusoidal: 1033 harmonic: 1474 Sorted by residual: dihedral pdb=" CA PHE A 78 " pdb=" C PHE A 78 " pdb=" N ARG A 79 " pdb=" CA ARG A 79 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LEU A 286 " pdb=" C LEU A 286 " pdb=" N GLN A 287 " pdb=" CA GLN A 287 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CB GLU A 415 " pdb=" CG GLU A 415 " pdb=" CD GLU A 415 " pdb=" OE1 GLU A 415 " ideal model delta sinusoidal sigma weight residual 0.00 -89.20 89.20 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 2504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 332 0.029 - 0.057: 170 0.057 - 0.086: 50 0.086 - 0.115: 35 0.115 - 0.143: 6 Chirality restraints: 593 Sorted by residual: chirality pdb=" CA GLU A 389 " pdb=" N GLU A 389 " pdb=" C GLU A 389 " pdb=" CB GLU A 389 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE A 424 " pdb=" N ILE A 424 " pdb=" C ILE A 424 " pdb=" CB ILE A 424 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE A 400 " pdb=" N ILE A 400 " pdb=" C ILE A 400 " pdb=" CB ILE A 400 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 590 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 432 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 433 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 433 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 433 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 293 " 0.003 2.00e-02 2.50e+03 1.16e-02 2.69e+00 pdb=" CG TYR A 293 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 293 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 293 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 293 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 293 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 293 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 293 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 298 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 299 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.021 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 220 2.73 - 3.27: 4234 3.27 - 3.81: 6561 3.81 - 4.36: 7432 4.36 - 4.90: 12749 Nonbonded interactions: 31196 Sorted by model distance: nonbonded pdb=" OH TYR A 44 " pdb=" O TYR A 411 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP A 247 " pdb=" OG SER A 254 " model vdw 2.244 3.040 nonbonded pdb=" O LEU A 291 " pdb=" NZ LYS A 304 " model vdw 2.253 3.120 nonbonded pdb=" NE1 TRP A 8 " pdb=" OE2 GLU A 63 " model vdw 2.303 3.120 nonbonded pdb=" N GLU A 450 " pdb=" OE1 GLU A 450 " model vdw 2.307 3.120 ... (remaining 31191 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: 1.530 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.003 0.054 4179 Z= 0.138 Angle : 0.953 38.687 5650 Z= 0.342 Chirality : 0.042 0.143 593 Planarity : 0.004 0.049 726 Dihedral : 13.232 89.198 1567 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.13 (0.39), residues: 501 helix: 0.86 (0.40), residues: 186 sheet: 0.08 (0.90), residues: 28 loop : -0.38 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.025 0.002 TYR A 293 PHE 0.007 0.001 PHE A 153 TRP 0.018 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4175) covalent geometry : angle 0.58560 ( 5644) hydrogen bonds : bond 0.19752 ( 163) hydrogen bonds : angle 8.27507 ( 426) metal coordination : bond 0.03770 ( 4) metal coordination : angle 23.09603 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7273 (mmp) cc_final: 0.6730 (mmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0734 time to fit residues: 5.9706 Evaluate side-chains 51 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.136294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.108470 restraints weight = 9048.314| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 5.32 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4179 Z= 0.144 Angle : 0.628 12.040 5650 Z= 0.299 Chirality : 0.043 0.154 593 Planarity : 0.004 0.032 726 Dihedral : 4.306 18.755 556 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.90 % Allowed : 7.87 % Favored : 91.24 % 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 aren not related in a simple way. whole: 0.35 (0.39), residues: 501 helix: 1.20 (0.40), residues: 176 sheet: 0.25 (0.76), residues: 51 loop : -0.37 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.012 0.001 TYR A 293 PHE 0.007 0.001 PHE A 335 TRP 0.006 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4175) covalent geometry : angle 0.58002 ( 5644) hydrogen bonds : bond 0.04467 ( 163) hydrogen bonds : angle 6.37499 ( 426) metal coordination : bond 0.01286 ( 4) metal coordination : angle 7.41565 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7315 (mmp) cc_final: 0.6637 (mmm) REVERT: A 296 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7785 (tm-30) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.0700 time to fit residues: 5.2256 Evaluate side-chains 52 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 0.0170 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.138509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.110398 restraints weight = 9120.442| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 5.45 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4179 Z= 0.101 Angle : 0.549 8.691 5650 Z= 0.270 Chirality : 0.042 0.141 593 Planarity : 0.004 0.034 726 Dihedral : 4.214 19.404 556 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.57 % Allowed : 11.01 % Favored : 87.42 % 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 aren not related in a simple way. whole: 0.40 (0.39), residues: 501 helix: 1.27 (0.40), residues: 176 sheet: 0.25 (0.77), residues: 51 loop : -0.36 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.008 0.001 TYR A 293 PHE 0.012 0.001 PHE A 157 TRP 0.010 0.001 TRP A 40 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 4175) covalent geometry : angle 0.52914 ( 5644) hydrogen bonds : bond 0.03533 ( 163) hydrogen bonds : angle 5.82537 ( 426) metal coordination : bond 0.00667 ( 4) metal coordination : angle 4.46510 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7324 (mmp) cc_final: 0.6822 (mmm) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.0662 time to fit residues: 5.4748 Evaluate side-chains 59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 21 optimal weight: 0.4980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.139186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.111123 restraints weight = 9116.716| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 5.47 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4179 Z= 0.097 Angle : 0.545 7.534 5650 Z= 0.267 Chirality : 0.042 0.151 593 Planarity : 0.004 0.037 726 Dihedral : 4.176 16.737 556 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.35 % Allowed : 13.48 % Favored : 85.17 % 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 aren not related in a simple way. whole: 0.37 (0.39), residues: 501 helix: 1.16 (0.40), residues: 176 sheet: 0.35 (0.78), residues: 51 loop : -0.33 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 4 TYR 0.006 0.001 TYR A 86 PHE 0.014 0.001 PHE A 157 TRP 0.010 0.001 TRP A 40 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 4175) covalent geometry : angle 0.53330 ( 5644) hydrogen bonds : bond 0.03340 ( 163) hydrogen bonds : angle 5.82178 ( 426) metal coordination : bond 0.00459 ( 4) metal coordination : angle 3.41969 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7308 (mmp) cc_final: 0.6783 (mmm) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.0658 time to fit residues: 5.2038 Evaluate side-chains 56 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.135235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.106890 restraints weight = 9350.516| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 5.51 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4179 Z= 0.152 Angle : 0.579 7.406 5650 Z= 0.288 Chirality : 0.043 0.144 593 Planarity : 0.004 0.035 726 Dihedral : 4.263 16.133 556 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.25 % Allowed : 13.26 % Favored : 84.49 % 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 aren not related in a simple way. whole: 0.29 (0.39), residues: 501 helix: 1.22 (0.40), residues: 175 sheet: 0.08 (0.68), residues: 59 loop : -0.44 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.010 0.001 TYR A 234 PHE 0.015 0.002 PHE A 157 TRP 0.010 0.001 TRP A 40 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4175) covalent geometry : angle 0.56812 ( 5644) hydrogen bonds : bond 0.03848 ( 163) hydrogen bonds : angle 5.78639 ( 426) metal coordination : bond 0.00717 ( 4) metal coordination : angle 3.50561 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8230 (ppp) cc_final: 0.7736 (ppp) REVERT: A 148 MET cc_start: 0.7367 (mmp) cc_final: 0.6939 (mmm) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.0776 time to fit residues: 5.7190 Evaluate side-chains 58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.136554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.108349 restraints weight = 9369.436| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 5.43 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4179 Z= 0.109 Angle : 0.559 7.898 5650 Z= 0.277 Chirality : 0.042 0.146 593 Planarity : 0.004 0.038 726 Dihedral : 4.174 16.216 556 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.02 % Allowed : 15.06 % Favored : 82.92 % 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 aren not related in a simple way. whole: 0.27 (0.39), residues: 501 helix: 1.22 (0.40), residues: 176 sheet: 0.10 (0.69), residues: 59 loop : -0.47 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.012 0.001 TYR A 293 PHE 0.011 0.001 PHE A 157 TRP 0.012 0.001 TRP A 40 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4175) covalent geometry : angle 0.55066 ( 5644) hydrogen bonds : bond 0.03389 ( 163) hydrogen bonds : angle 5.63094 ( 426) metal coordination : bond 0.00468 ( 4) metal coordination : angle 2.92476 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6139 (ppp) cc_final: 0.5926 (ppp) REVERT: A 65 MET cc_start: 0.8190 (ppp) cc_final: 0.7623 (ppp) REVERT: A 85 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7499 (tt) REVERT: A 148 MET cc_start: 0.7372 (mmp) cc_final: 0.6931 (mmm) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.0700 time to fit residues: 4.9806 Evaluate side-chains 59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.138368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109528 restraints weight = 10029.574| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 5.79 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4179 Z= 0.108 Angle : 0.553 7.868 5650 Z= 0.275 Chirality : 0.042 0.147 593 Planarity : 0.004 0.038 726 Dihedral : 4.124 15.930 556 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.02 % Allowed : 15.73 % Favored : 82.25 % 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 aren not related in a simple way. whole: 0.23 (0.39), residues: 501 helix: 1.11 (0.40), residues: 176 sheet: 0.14 (0.69), residues: 59 loop : -0.46 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 79 TYR 0.015 0.001 TYR A 293 PHE 0.008 0.001 PHE A 157 TRP 0.015 0.001 TRP A 40 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4175) covalent geometry : angle 0.54620 ( 5644) hydrogen bonds : bond 0.03299 ( 163) hydrogen bonds : angle 5.63721 ( 426) metal coordination : bond 0.00453 ( 4) metal coordination : angle 2.71233 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7484 (tt) REVERT: A 148 MET cc_start: 0.7368 (mmp) cc_final: 0.6929 (mmm) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.0690 time to fit residues: 5.0647 Evaluate side-chains 58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.134439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.105712 restraints weight = 10131.777| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 5.72 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4179 Z= 0.210 Angle : 0.636 7.362 5650 Z= 0.321 Chirality : 0.045 0.140 593 Planarity : 0.004 0.034 726 Dihedral : 4.567 18.700 556 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.57 % Allowed : 16.63 % Favored : 81.80 % 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 aren not related in a simple way. whole: -0.20 (0.38), residues: 501 helix: 0.97 (0.40), residues: 175 sheet: -0.64 (0.68), residues: 45 loop : -0.73 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 452 TYR 0.036 0.002 TYR A 293 PHE 0.011 0.002 PHE A 78 TRP 0.011 0.002 TRP A 40 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 4175) covalent geometry : angle 0.62514 ( 5644) hydrogen bonds : bond 0.04196 ( 163) hydrogen bonds : angle 6.01689 ( 426) metal coordination : bond 0.00983 ( 4) metal coordination : angle 3.63556 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7554 (tt) REVERT: A 148 MET cc_start: 0.7462 (mmp) cc_final: 0.6932 (mmm) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.0705 time to fit residues: 4.6869 Evaluate side-chains 55 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.0020 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.137974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.108663 restraints weight = 9370.099| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 5.61 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4179 Z= 0.105 Angle : 0.571 7.672 5650 Z= 0.284 Chirality : 0.042 0.155 593 Planarity : 0.004 0.037 726 Dihedral : 4.310 16.980 556 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.25 % Allowed : 15.73 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.39), residues: 501 helix: 1.00 (0.40), residues: 175 sheet: -0.06 (0.68), residues: 61 loop : -0.66 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.019 0.001 TYR A 293 PHE 0.007 0.001 PHE A 78 TRP 0.022 0.001 TRP A 40 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 4175) covalent geometry : angle 0.56390 ( 5644) hydrogen bonds : bond 0.03289 ( 163) hydrogen bonds : angle 5.82638 ( 426) metal coordination : bond 0.00446 ( 4) metal coordination : angle 2.80210 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7512 (tt) REVERT: A 148 MET cc_start: 0.7489 (mmp) cc_final: 0.6960 (mmm) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.0680 time to fit residues: 4.9620 Evaluate side-chains 56 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.137688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.108707 restraints weight = 9857.674| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 5.76 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4179 Z= 0.119 Angle : 0.603 10.907 5650 Z= 0.304 Chirality : 0.044 0.179 593 Planarity : 0.004 0.037 726 Dihedral : 4.355 20.916 556 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.80 % Allowed : 16.85 % Favored : 81.35 % 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 aren not related in a simple way. whole: -0.08 (0.39), residues: 501 helix: 0.94 (0.40), residues: 176 sheet: -0.37 (0.69), residues: 51 loop : -0.61 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.018 0.001 TYR A 293 PHE 0.009 0.001 PHE A 78 TRP 0.018 0.001 TRP A 40 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4175) covalent geometry : angle 0.59649 ( 5644) hydrogen bonds : bond 0.03446 ( 163) hydrogen bonds : angle 5.90181 ( 426) metal coordination : bond 0.00521 ( 4) metal coordination : angle 2.67751 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7470 (tt) REVERT: A 148 MET cc_start: 0.7311 (mmp) cc_final: 0.6625 (mmm) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.0720 time to fit residues: 4.9684 Evaluate side-chains 56 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.138378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.109342 restraints weight = 9933.017| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 5.82 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4179 Z= 0.109 Angle : 0.579 7.591 5650 Z= 0.292 Chirality : 0.043 0.171 593 Planarity : 0.004 0.038 726 Dihedral : 4.259 20.225 556 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.80 % Allowed : 16.63 % Favored : 81.57 % 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 aren not related in a simple way. whole: -0.02 (0.39), residues: 501 helix: 1.01 (0.41), residues: 176 sheet: -0.30 (0.70), residues: 51 loop : -0.61 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.015 0.001 TYR A 293 PHE 0.008 0.001 PHE A 78 TRP 0.016 0.001 TRP A 40 HIS 0.002 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4175) covalent geometry : angle 0.57441 ( 5644) hydrogen bonds : bond 0.03310 ( 163) hydrogen bonds : angle 5.86086 ( 426) metal coordination : bond 0.00445 ( 4) metal coordination : angle 2.35259 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1124.25 seconds wall clock time: 20 minutes 3.91 seconds (1203.91 seconds total)