Starting phenix.real_space_refine on Sat May 10 06:55:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hs2_34983/05_2025/8hs2_34983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hs2_34983/05_2025/8hs2_34983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hs2_34983/05_2025/8hs2_34983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hs2_34983/05_2025/8hs2_34983.map" model { file = "/net/cci-nas-00/data/ceres_data/8hs2_34983/05_2025/8hs2_34983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hs2_34983/05_2025/8hs2_34983.cif" } resolution = 3.08 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= 0.012 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 3487 2.51 5 N 930 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5456 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1617 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1623 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "R" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2216 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.51, per 1000 atoms: 0.64 Number of scatterers: 5456 At special positions: 0 Unit cell: (69.888, 92.352, 138.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1005 8.00 N 930 7.00 C 3487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 374 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 122 " distance=2.03 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: 1.16 Conformation dependent library (CDL) restraints added in 661.0 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 13 sheets defined 39.1% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.753A pdb=" N TYR B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.666A pdb=" N SER B 110 " --> pdb=" O PRO B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.688A pdb=" N LEU C 411 " --> pdb=" O THR C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.538A pdb=" N HIS C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 49 removed outlier: 4.059A pdb=" N ALA R 39 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 81 Processing helix chain 'R' and resid 86 through 116 Proline residue: R 107 - end of helix removed outlier: 4.233A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 122 No H-bonds generated for 'chain 'R' and resid 120 through 122' Processing helix chain 'R' and resid 123 through 151 removed outlier: 3.708A pdb=" N VAL R 127 " --> pdb=" O ALA R 123 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER R 137 " --> pdb=" O ASN R 133 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE R 138 " --> pdb=" O MET R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 187 removed outlier: 3.815A pdb=" N ALA R 167 " --> pdb=" O GLN R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 205 removed outlier: 3.913A pdb=" N VAL R 202 " --> pdb=" O PHE R 198 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU R 203 " --> pdb=" O ALA R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 225 Processing helix chain 'R' and resid 229 through 254 Processing helix chain 'R' and resid 254 through 267 removed outlier: 3.527A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 293 removed outlier: 4.380A pdb=" N SER R 290 " --> pdb=" O SER R 286 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS R 291 " --> pdb=" O SER R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 301 removed outlier: 3.967A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 317 removed outlier: 4.099A pdb=" N ALA R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.674A pdb=" N ILE B 53 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE B 69 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.161A pdb=" N TYR B 131 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA B 119 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE B 129 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 153 removed outlier: 4.015A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 165 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 169 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 204 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 153 removed outlier: 4.015A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 165 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 169 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 204 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 198 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 292 through 293 removed outlier: 6.678A pdb=" N THR C 355 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AA9, first strand: chain 'C' and resid 319 through 321 Processing sheet with id=AB1, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AB2, first strand: chain 'C' and resid 371 through 372 Processing sheet with id=AB3, first strand: chain 'C' and resid 402 through 404 removed outlier: 3.742A pdb=" N VAL C 419 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR C 459 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 431 through 435 removed outlier: 4.009A pdb=" N LYS C 493 " --> pdb=" O CYS C 480 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 482 " --> pdb=" O VAL C 491 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 879 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: 1.66 Time building geometry restraints manager: 1.38 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: 1723 1.34 - 1.46: 1339 1.46 - 1.58: 2481 1.58 - 1.70: 0 1.70 - 1.81: 44 Bond restraints: 5587 Sorted by residual: bond pdb=" CB GLN B 200 " pdb=" CG GLN B 200 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.77e+00 bond pdb=" CB LYS C 435 " pdb=" CG LYS C 435 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CA ASP R 269 " pdb=" CB ASP R 269 " ideal model delta sigma weight residual 1.529 1.555 -0.025 1.74e-02 3.30e+03 2.13e+00 bond pdb=" CB ASP B 108 " pdb=" CG ASP B 108 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" CB ASP R 269 " pdb=" CG ASP R 269 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.95e+00 ... (remaining 5582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 7437 2.23 - 4.46: 129 4.46 - 6.69: 40 6.69 - 8.92: 5 8.92 - 11.15: 2 Bond angle restraints: 7613 Sorted by residual: angle pdb=" CA GLN B 200 " pdb=" CB GLN B 200 " pdb=" CG GLN B 200 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CA ARG C 442 " pdb=" CB ARG C 442 " pdb=" CG ARG C 442 " ideal model delta sigma weight residual 114.10 122.81 -8.71 2.00e+00 2.50e-01 1.90e+01 angle pdb=" CA LYS C 433 " pdb=" CB LYS C 433 " pdb=" CG LYS C 433 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB LYS C 435 " pdb=" CG LYS C 435 " pdb=" CD LYS C 435 " ideal model delta sigma weight residual 111.30 119.88 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA ASP R 269 " pdb=" CB ASP R 269 " pdb=" CG ASP R 269 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 ... (remaining 7608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2921 17.85 - 35.70: 299 35.70 - 53.55: 71 53.55 - 71.40: 4 71.40 - 89.25: 7 Dihedral angle restraints: 3302 sinusoidal: 1237 harmonic: 2065 Sorted by residual: dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 122 " pdb=" CB CYS R 122 " ideal model delta sinusoidal sigma weight residual -86.00 -175.25 89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CA LEU R 229 " pdb=" C LEU R 229 " pdb=" N HIS R 230 " pdb=" CA HIS R 230 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA SER C 402 " pdb=" C SER C 402 " pdb=" N ILE C 403 " pdb=" CA ILE C 403 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 3299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 665 0.044 - 0.088: 153 0.088 - 0.131: 61 0.131 - 0.175: 9 0.175 - 0.219: 4 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA TYR C 426 " pdb=" N TYR C 426 " pdb=" C TYR C 426 " pdb=" CB TYR C 426 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL R 32 " pdb=" CA VAL R 32 " pdb=" CG1 VAL R 32 " pdb=" CG2 VAL R 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO C 427 " pdb=" N PRO C 427 " pdb=" C PRO C 427 " pdb=" CB PRO C 427 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 889 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 269 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ASP R 269 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP R 269 " 0.015 2.00e-02 2.50e+03 pdb=" N MET R 270 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 344 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 345 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 108 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" CG ASP B 108 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP B 108 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 108 " -0.012 2.00e-02 2.50e+03 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 303 2.73 - 3.27: 5506 3.27 - 3.82: 9267 3.82 - 4.36: 10235 4.36 - 4.90: 18460 Nonbonded interactions: 43771 Sorted by model distance: nonbonded pdb=" O LEU C 392 " pdb=" OH TYR C 426 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR C 289 " pdb=" OE2 GLU C 379 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP C 453 " pdb=" OG1 THR C 458 " model vdw 2.331 3.040 nonbonded pdb=" OG SER R 88 " pdb=" OD2 ASP R 147 " model vdw 2.333 3.040 nonbonded pdb=" N GLN R 305 " pdb=" OE1 GLN R 305 " model vdw 2.334 3.120 ... (remaining 43766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.710 Find NCS groups from input model: 0.050 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.004 0.050 5592 Z= 0.177 Angle : 0.777 11.154 7623 Z= 0.410 Chirality : 0.046 0.219 892 Planarity : 0.005 0.054 954 Dihedral : 14.964 85.417 1963 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.17 % Allowed : 19.31 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.10 (0.31), residues: 708 helix: 1.52 (0.32), residues: 244 sheet: 0.12 (0.38), residues: 186 loop : -1.28 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.005 0.001 HIS C 475 PHE 0.014 0.001 PHE B 69 TYR 0.008 0.001 TYR B 66 ARG 0.005 0.001 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.15069 ( 302) hydrogen bonds : angle 7.51785 ( 879) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.95197 ( 10) covalent geometry : bond 0.00404 ( 5587) covalent geometry : angle 0.77699 ( 7613) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: R 133 ASN cc_start: 0.9205 (t0) cc_final: 0.8943 (t0) REVERT: R 162 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7903 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.2463 time to fit residues: 26.7787 Evaluate side-chains 83 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.068837 restraints weight = 11239.887| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.04 r_work: 0.2805 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5592 Z= 0.119 Angle : 0.570 7.379 7623 Z= 0.299 Chirality : 0.042 0.175 892 Planarity : 0.005 0.043 954 Dihedral : 4.128 19.940 774 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.32 % Allowed : 17.66 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.49 (0.32), residues: 708 helix: 2.23 (0.33), residues: 238 sheet: -0.14 (0.36), residues: 212 loop : -1.06 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 139 HIS 0.004 0.001 HIS R 126 PHE 0.011 0.001 PHE B 69 TYR 0.010 0.001 TYR C 318 ARG 0.003 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 302) hydrogen bonds : angle 5.18105 ( 879) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.98427 ( 10) covalent geometry : bond 0.00262 ( 5587) covalent geometry : angle 0.56963 ( 7613) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9195 (m-30) cc_final: 0.8692 (m-30) REVERT: B 151 TYR cc_start: 0.8505 (m-80) cc_final: 0.8111 (m-80) REVERT: B 200 GLN cc_start: 0.7722 (pp30) cc_final: 0.7404 (pp30) REVERT: C 335 TYR cc_start: 0.8330 (p90) cc_final: 0.8116 (p90) REVERT: C 347 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7912 (ptp90) REVERT: C 378 ASN cc_start: 0.9143 (t0) cc_final: 0.8853 (t0) REVERT: C 389 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8568 (mmmm) REVERT: C 391 GLU cc_start: 0.8974 (pm20) cc_final: 0.8604 (pm20) REVERT: C 422 MET cc_start: 0.9331 (pmm) cc_final: 0.9112 (pmm) REVERT: C 433 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8643 (tmtt) REVERT: C 442 ARG cc_start: 0.7813 (mpt180) cc_final: 0.7598 (mpt180) REVERT: C 480 CYS cc_start: 0.6483 (p) cc_final: 0.6227 (p) REVERT: R 162 ARG cc_start: 0.8439 (mmt-90) cc_final: 0.8147 (mmt-90) outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.2100 time to fit residues: 25.7554 Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 270 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 35 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.104879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.067909 restraints weight = 11248.964| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.02 r_work: 0.2789 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5592 Z= 0.132 Angle : 0.549 6.346 7623 Z= 0.286 Chirality : 0.042 0.161 892 Planarity : 0.004 0.040 954 Dihedral : 3.951 16.507 774 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.65 % Allowed : 18.65 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.69 (0.32), residues: 708 helix: 2.46 (0.33), residues: 238 sheet: -0.06 (0.35), residues: 214 loop : -1.00 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 139 HIS 0.005 0.001 HIS R 126 PHE 0.012 0.001 PHE B 69 TYR 0.016 0.001 TYR C 472 ARG 0.004 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 302) hydrogen bonds : angle 4.82455 ( 879) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.87730 ( 10) covalent geometry : bond 0.00298 ( 5587) covalent geometry : angle 0.54877 ( 7613) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9172 (m-30) cc_final: 0.8707 (m-30) REVERT: B 200 GLN cc_start: 0.7812 (pp30) cc_final: 0.7444 (pp30) REVERT: C 378 ASN cc_start: 0.9117 (t0) cc_final: 0.8792 (t0) REVERT: C 389 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8445 (mmmm) REVERT: C 391 GLU cc_start: 0.8993 (pm20) cc_final: 0.8608 (pm20) REVERT: C 403 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8622 (mm) REVERT: C 433 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8495 (tmtt) REVERT: C 435 LYS cc_start: 0.9153 (tppt) cc_final: 0.8924 (tppt) REVERT: C 441 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7560 (tpt-90) REVERT: C 442 ARG cc_start: 0.7755 (mpt180) cc_final: 0.7519 (mpt180) REVERT: C 480 CYS cc_start: 0.6425 (p) cc_final: 0.6006 (p) REVERT: R 272 HIS cc_start: 0.7479 (t70) cc_final: 0.6877 (t-90) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.2058 time to fit residues: 25.2990 Evaluate side-chains 91 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.067452 restraints weight = 11480.385| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.09 r_work: 0.2782 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5592 Z= 0.134 Angle : 0.552 6.120 7623 Z= 0.288 Chirality : 0.042 0.162 892 Planarity : 0.004 0.039 954 Dihedral : 3.915 15.306 774 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.31 % Allowed : 19.31 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.76 (0.32), residues: 708 helix: 2.55 (0.33), residues: 239 sheet: -0.08 (0.35), residues: 214 loop : -0.93 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 183 HIS 0.005 0.001 HIS R 126 PHE 0.018 0.001 PHE C 495 TYR 0.018 0.001 TYR C 472 ARG 0.004 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 302) hydrogen bonds : angle 4.69645 ( 879) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.91488 ( 10) covalent geometry : bond 0.00307 ( 5587) covalent geometry : angle 0.55127 ( 7613) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.735 Fit side-chains REVERT: B 109 ASP cc_start: 0.9182 (m-30) cc_final: 0.8703 (m-30) REVERT: B 177 GLU cc_start: 0.8367 (pm20) cc_final: 0.7826 (tp30) REVERT: B 191 ASP cc_start: 0.8430 (t0) cc_final: 0.8166 (t0) REVERT: C 347 ARG cc_start: 0.8242 (ptp90) cc_final: 0.7964 (ptp90) REVERT: C 365 GLU cc_start: 0.8513 (mp0) cc_final: 0.7949 (mp0) REVERT: C 378 ASN cc_start: 0.9129 (t0) cc_final: 0.8806 (t0) REVERT: C 389 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8541 (mmmm) REVERT: C 391 GLU cc_start: 0.9025 (pm20) cc_final: 0.8650 (pm20) REVERT: C 433 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8269 (tmtt) REVERT: C 435 LYS cc_start: 0.9224 (tppt) cc_final: 0.8928 (tppt) REVERT: C 441 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7536 (tpt-90) REVERT: C 442 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7462 (mpt180) REVERT: R 162 ARG cc_start: 0.8378 (mmt-90) cc_final: 0.8172 (mmt-90) REVERT: R 272 HIS cc_start: 0.7578 (t70) cc_final: 0.7287 (t-90) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.2225 time to fit residues: 25.4849 Evaluate side-chains 96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.101183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.063359 restraints weight = 11364.846| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.07 r_work: 0.2711 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 5592 Z= 0.284 Angle : 0.623 7.374 7623 Z= 0.323 Chirality : 0.045 0.183 892 Planarity : 0.004 0.038 954 Dihedral : 4.150 17.137 774 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.31 % Allowed : 19.80 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.64 (0.32), residues: 708 helix: 2.46 (0.33), residues: 239 sheet: -0.22 (0.35), residues: 214 loop : -0.94 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 PHE 0.020 0.002 PHE B 69 TYR 0.019 0.002 TYR B 151 ARG 0.004 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 302) hydrogen bonds : angle 4.84116 ( 879) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.05544 ( 10) covalent geometry : bond 0.00656 ( 5587) covalent geometry : angle 0.62261 ( 7613) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.602 Fit side-chains REVERT: B 109 ASP cc_start: 0.9218 (m-30) cc_final: 0.8711 (m-30) REVERT: B 177 GLU cc_start: 0.8379 (pm20) cc_final: 0.7666 (tp30) REVERT: B 191 ASP cc_start: 0.8568 (t0) cc_final: 0.8324 (t0) REVERT: B 200 GLN cc_start: 0.7870 (pp30) cc_final: 0.7443 (pp30) REVERT: C 347 ARG cc_start: 0.8241 (ptp90) cc_final: 0.8038 (ptp90) REVERT: C 365 GLU cc_start: 0.8498 (mp0) cc_final: 0.8000 (mp0) REVERT: C 378 ASN cc_start: 0.9223 (t0) cc_final: 0.8860 (t0) REVERT: C 389 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8451 (mmmm) REVERT: C 391 GLU cc_start: 0.8987 (pm20) cc_final: 0.8610 (pm20) REVERT: C 433 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8276 (tmtt) REVERT: C 435 LYS cc_start: 0.9174 (tppt) cc_final: 0.8893 (tppt) REVERT: C 442 ARG cc_start: 0.7810 (mpt180) cc_final: 0.7525 (mpt180) REVERT: R 272 HIS cc_start: 0.7763 (t70) cc_final: 0.7503 (t-90) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.2071 time to fit residues: 24.9293 Evaluate side-chains 99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.102345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.064823 restraints weight = 11316.329| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.99 r_work: 0.2738 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5592 Z= 0.195 Angle : 0.586 6.312 7623 Z= 0.304 Chirality : 0.043 0.173 892 Planarity : 0.004 0.037 954 Dihedral : 4.133 17.746 774 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.15 % Allowed : 20.96 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.63 (0.32), residues: 708 helix: 2.41 (0.33), residues: 245 sheet: -0.19 (0.35), residues: 214 loop : -1.04 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 PHE 0.015 0.001 PHE B 69 TYR 0.014 0.001 TYR C 426 ARG 0.003 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 302) hydrogen bonds : angle 4.73333 ( 879) SS BOND : bond 0.00309 ( 5) SS BOND : angle 0.96584 ( 10) covalent geometry : bond 0.00450 ( 5587) covalent geometry : angle 0.58510 ( 7613) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: B 200 GLN cc_start: 0.7941 (pp30) cc_final: 0.7486 (pp30) REVERT: C 347 ARG cc_start: 0.8314 (ptp90) cc_final: 0.7983 (ptp90) REVERT: C 365 GLU cc_start: 0.8520 (mp0) cc_final: 0.7895 (mp0) REVERT: C 378 ASN cc_start: 0.9185 (t0) cc_final: 0.8832 (t0) REVERT: C 389 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8597 (mmmm) REVERT: C 391 GLU cc_start: 0.8957 (pm20) cc_final: 0.8577 (pm20) REVERT: C 409 GLU cc_start: 0.9559 (pm20) cc_final: 0.9334 (pm20) REVERT: C 433 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8621 (tmtt) REVERT: C 442 ARG cc_start: 0.7799 (mpt180) cc_final: 0.7558 (mpt180) REVERT: R 272 HIS cc_start: 0.7745 (t70) cc_final: 0.7406 (t-90) outliers start: 13 outliers final: 12 residues processed: 95 average time/residue: 0.2163 time to fit residues: 25.5738 Evaluate side-chains 98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.103416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.065985 restraints weight = 11344.503| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.05 r_work: 0.2752 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5592 Z= 0.146 Angle : 0.594 9.775 7623 Z= 0.307 Chirality : 0.043 0.170 892 Planarity : 0.004 0.037 954 Dihedral : 4.057 17.565 774 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.97 % Allowed : 20.46 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.70 (0.32), residues: 708 helix: 2.47 (0.33), residues: 245 sheet: -0.17 (0.35), residues: 214 loop : -0.98 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 PHE 0.010 0.001 PHE B 69 TYR 0.021 0.001 TYR C 472 ARG 0.003 0.000 ARG C 410 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 302) hydrogen bonds : angle 4.59742 ( 879) SS BOND : bond 0.00183 ( 5) SS BOND : angle 0.93913 ( 10) covalent geometry : bond 0.00336 ( 5587) covalent geometry : angle 0.59300 ( 7613) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.565 Fit side-chains REVERT: B 177 GLU cc_start: 0.8480 (pm20) cc_final: 0.7815 (tp30) REVERT: B 200 GLN cc_start: 0.7911 (pp30) cc_final: 0.7465 (pp30) REVERT: C 347 ARG cc_start: 0.8286 (ptp90) cc_final: 0.7971 (ptp90) REVERT: C 365 GLU cc_start: 0.8499 (mp0) cc_final: 0.7919 (mp0) REVERT: C 378 ASN cc_start: 0.9165 (t0) cc_final: 0.8822 (t0) REVERT: C 389 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8571 (mmmm) REVERT: C 391 GLU cc_start: 0.8970 (pm20) cc_final: 0.8569 (pm20) REVERT: C 433 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8269 (tmtt) REVERT: C 435 LYS cc_start: 0.9206 (tppt) cc_final: 0.8905 (tppt) REVERT: C 441 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7700 (tpt-90) REVERT: C 442 ARG cc_start: 0.7758 (mpt180) cc_final: 0.7453 (mpt180) REVERT: R 231 GLN cc_start: 0.9147 (pp30) cc_final: 0.8901 (pp30) REVERT: R 272 HIS cc_start: 0.7696 (t70) cc_final: 0.7332 (t-90) outliers start: 18 outliers final: 14 residues processed: 102 average time/residue: 0.2041 time to fit residues: 26.0215 Evaluate side-chains 98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 30 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.104493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.066917 restraints weight = 11361.320| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.07 r_work: 0.2778 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5592 Z= 0.123 Angle : 0.593 11.742 7623 Z= 0.302 Chirality : 0.043 0.194 892 Planarity : 0.004 0.038 954 Dihedral : 3.990 18.222 774 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.31 % Allowed : 20.46 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.79 (0.32), residues: 708 helix: 2.54 (0.33), residues: 245 sheet: -0.10 (0.35), residues: 214 loop : -0.94 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 PHE 0.014 0.001 PHE C 495 TYR 0.028 0.001 TYR B 174 ARG 0.004 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 302) hydrogen bonds : angle 4.49697 ( 879) SS BOND : bond 0.00279 ( 5) SS BOND : angle 0.76424 ( 10) covalent geometry : bond 0.00279 ( 5587) covalent geometry : angle 0.59292 ( 7613) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.623 Fit side-chains REVERT: B 200 GLN cc_start: 0.8005 (pp30) cc_final: 0.7557 (pp30) REVERT: C 347 ARG cc_start: 0.8296 (ptp90) cc_final: 0.7996 (ptp90) REVERT: C 365 GLU cc_start: 0.8466 (mp0) cc_final: 0.7902 (mp0) REVERT: C 378 ASN cc_start: 0.9149 (t0) cc_final: 0.8821 (t0) REVERT: C 389 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8574 (mmmm) REVERT: C 391 GLU cc_start: 0.8945 (pm20) cc_final: 0.8598 (pm20) REVERT: C 403 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8327 (mm) REVERT: C 433 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8402 (tmtt) REVERT: C 435 LYS cc_start: 0.9242 (tppt) cc_final: 0.8926 (tppt) REVERT: C 441 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7749 (tpt-90) REVERT: C 442 ARG cc_start: 0.7776 (mpt180) cc_final: 0.7518 (mpt180) REVERT: C 480 CYS cc_start: 0.6136 (p) cc_final: 0.5807 (p) REVERT: R 231 GLN cc_start: 0.9112 (pp30) cc_final: 0.8874 (pp30) REVERT: R 272 HIS cc_start: 0.7612 (t70) cc_final: 0.7269 (t-90) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.2127 time to fit residues: 25.9065 Evaluate side-chains 98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 0.0040 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.104314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.066956 restraints weight = 11283.478| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.06 r_work: 0.2775 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5592 Z= 0.141 Angle : 0.617 11.075 7623 Z= 0.315 Chirality : 0.043 0.200 892 Planarity : 0.004 0.039 954 Dihedral : 4.025 18.902 774 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.48 % Allowed : 21.78 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.84 (0.32), residues: 708 helix: 2.56 (0.33), residues: 245 sheet: -0.08 (0.35), residues: 214 loop : -0.88 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 PHE 0.011 0.001 PHE C 495 TYR 0.028 0.001 TYR B 174 ARG 0.006 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 302) hydrogen bonds : angle 4.47702 ( 879) SS BOND : bond 0.00211 ( 5) SS BOND : angle 0.82757 ( 10) covalent geometry : bond 0.00328 ( 5587) covalent geometry : angle 0.61663 ( 7613) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.617 Fit side-chains REVERT: B 109 ASP cc_start: 0.9131 (m-30) cc_final: 0.8622 (m-30) REVERT: B 131 TYR cc_start: 0.8997 (m-80) cc_final: 0.8789 (m-80) REVERT: B 174 TYR cc_start: 0.8525 (p90) cc_final: 0.8278 (p90) REVERT: C 347 ARG cc_start: 0.8298 (ptp90) cc_final: 0.7975 (ptp90) REVERT: C 365 GLU cc_start: 0.8441 (mp0) cc_final: 0.7846 (mp0) REVERT: C 378 ASN cc_start: 0.9167 (t0) cc_final: 0.8859 (t0) REVERT: C 389 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8572 (mmmm) REVERT: C 391 GLU cc_start: 0.8964 (pm20) cc_final: 0.8605 (pm20) REVERT: C 403 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8344 (mm) REVERT: C 433 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8570 (tmtt) REVERT: C 435 LYS cc_start: 0.9219 (tppt) cc_final: 0.8906 (tppt) REVERT: C 441 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7428 (tpt-90) REVERT: C 480 CYS cc_start: 0.6050 (p) cc_final: 0.5714 (p) REVERT: R 231 GLN cc_start: 0.9124 (pp30) cc_final: 0.8890 (pp30) REVERT: R 272 HIS cc_start: 0.7580 (t70) cc_final: 0.7199 (t70) outliers start: 15 outliers final: 13 residues processed: 96 average time/residue: 0.2093 time to fit residues: 25.2554 Evaluate side-chains 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.067127 restraints weight = 11331.770| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.03 r_work: 0.2789 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5592 Z= 0.137 Angle : 0.628 10.808 7623 Z= 0.321 Chirality : 0.043 0.209 892 Planarity : 0.005 0.055 954 Dihedral : 4.048 19.422 774 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.31 % Allowed : 21.62 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.89 (0.32), residues: 708 helix: 2.54 (0.33), residues: 245 sheet: 0.02 (0.35), residues: 214 loop : -0.85 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 PHE 0.011 0.001 PHE B 69 TYR 0.036 0.002 TYR B 151 ARG 0.006 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 302) hydrogen bonds : angle 4.43443 ( 879) SS BOND : bond 0.00176 ( 5) SS BOND : angle 0.78882 ( 10) covalent geometry : bond 0.00319 ( 5587) covalent geometry : angle 0.62735 ( 7613) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.576 Fit side-chains REVERT: B 109 ASP cc_start: 0.9139 (m-30) cc_final: 0.8632 (m-30) REVERT: B 174 TYR cc_start: 0.8568 (p90) cc_final: 0.8275 (p90) REVERT: B 200 GLN cc_start: 0.8096 (pp30) cc_final: 0.7661 (pp30) REVERT: C 347 ARG cc_start: 0.8335 (ptp90) cc_final: 0.7996 (ptp90) REVERT: C 365 GLU cc_start: 0.8446 (mp0) cc_final: 0.7848 (mp0) REVERT: C 378 ASN cc_start: 0.9153 (t0) cc_final: 0.8875 (t0) REVERT: C 389 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8631 (mmmm) REVERT: C 391 GLU cc_start: 0.8990 (pm20) cc_final: 0.8654 (pm20) REVERT: C 403 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8304 (mm) REVERT: C 433 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8609 (tmtt) REVERT: C 435 LYS cc_start: 0.9184 (tppt) cc_final: 0.8900 (tppt) REVERT: C 441 ARG cc_start: 0.7825 (mmm160) cc_final: 0.7498 (tpt-90) REVERT: C 480 CYS cc_start: 0.5981 (p) cc_final: 0.5697 (p) REVERT: R 231 GLN cc_start: 0.9099 (pp30) cc_final: 0.8871 (pp30) REVERT: R 272 HIS cc_start: 0.7552 (t70) cc_final: 0.7242 (t-90) REVERT: R 305 GLN cc_start: 0.8466 (pm20) cc_final: 0.8234 (pm20) outliers start: 14 outliers final: 12 residues processed: 99 average time/residue: 0.2119 time to fit residues: 26.2577 Evaluate side-chains 100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 0.0270 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.105497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.068093 restraints weight = 11295.692| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.98 r_work: 0.2812 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5592 Z= 0.126 Angle : 0.631 10.578 7623 Z= 0.322 Chirality : 0.043 0.199 892 Planarity : 0.004 0.039 954 Dihedral : 4.030 22.412 774 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.15 % Allowed : 21.95 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.32), residues: 708 helix: 2.58 (0.33), residues: 245 sheet: -0.05 (0.35), residues: 212 loop : -0.76 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 183 HIS 0.005 0.001 HIS R 126 PHE 0.009 0.001 PHE C 495 TYR 0.026 0.001 TYR B 174 ARG 0.006 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 302) hydrogen bonds : angle 4.35337 ( 879) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.81102 ( 10) covalent geometry : bond 0.00289 ( 5587) covalent geometry : angle 0.63050 ( 7613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.15 seconds wall clock time: 52 minutes 51.06 seconds (3171.06 seconds total)