Starting phenix.real_space_refine on Tue Feb 11 06:53:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8el8_28224/02_2025/8el8_28224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8el8_28224/02_2025/8el8_28224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8el8_28224/02_2025/8el8_28224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8el8_28224/02_2025/8el8_28224.map" model { file = "/net/cci-nas-00/data/ceres_data/8el8_28224/02_2025/8el8_28224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8el8_28224/02_2025/8el8_28224.cif" } resolution = 3.2 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= -0.001 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 2868 2.51 5 N 778 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4467 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1046 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 5 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3421 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 15, 'TRANS': 441} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 1, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 3.01, per 1000 atoms: 0.67 Number of scatterers: 4467 At special positions: 0 Unit cell: (53.6823, 80.9495, 110.773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 792 8.00 N 778 7.00 C 2868 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: 1.58 Conformation dependent library (CDL) restraints added in 631.7 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 67.2% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.680A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.507A pdb=" N ALA A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.962A pdb=" N THR A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.674A pdb=" N TYR A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.622A pdb=" N GLY B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 removed outlier: 3.615A pdb=" N GLU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 39 through 54 removed outlier: 3.519A pdb=" N LEU B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.923A pdb=" N THR B 84 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 removed outlier: 3.577A pdb=" N ILE B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 128 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.674A pdb=" N GLN B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 3.909A pdb=" N LYS B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.754A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 238 Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.675A pdb=" N VAL B 255 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 286 removed outlier: 4.137A pdb=" N GLU B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 removed outlier: 4.722A pdb=" N ASP B 294 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 295 " --> pdb=" O CYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.574A pdb=" N HIS B 343 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS B 355 " --> pdb=" O LYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 377 removed outlier: 4.072A pdb=" N THR B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Proline residue: B 365 - end of helix removed outlier: 3.729A pdb=" N ALA B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 404 through 412 Processing helix chain 'B' and resid 417 through 432 removed outlier: 3.708A pdb=" N LYS B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 removed outlier: 3.596A pdb=" N LYS B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 455 removed outlier: 5.193A pdb=" N GLY B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.500A pdb=" N LYS B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.295A pdb=" N LEU A 46 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL A 234 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 277 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR A 233 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 274 " --> pdb=" O TYR A 347 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS A 349 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A 276 " --> pdb=" O HIS A 349 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 675 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: 1.04 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 853 1.33 - 1.45: 998 1.45 - 1.57: 2647 1.57 - 1.68: 2 1.68 - 1.80: 38 Bond restraints: 4538 Sorted by residual: bond pdb=" O3P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.476 0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" O2P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.480 0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" O1P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" OG1 TPO B 473 " pdb=" P TPO B 473 " ideal model delta sigma weight residual 1.717 1.598 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CA LYS B 479 " pdb=" C LYS B 479 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.35e-02 5.49e+03 1.67e+01 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 6000 1.87 - 3.74: 131 3.74 - 5.61: 26 5.61 - 7.48: 7 7.48 - 9.35: 3 Bond angle restraints: 6167 Sorted by residual: angle pdb=" N ARG B 183 " pdb=" CA ARG B 183 " pdb=" C ARG B 183 " ideal model delta sigma weight residual 111.07 118.31 -7.24 1.07e+00 8.73e-01 4.58e+01 angle pdb=" N TYR B 442 " pdb=" CA TYR B 442 " pdb=" C TYR B 442 " ideal model delta sigma weight residual 111.36 117.49 -6.13 1.09e+00 8.42e-01 3.16e+01 angle pdb=" N THR B 443 " pdb=" CA THR B 443 " pdb=" C THR B 443 " ideal model delta sigma weight residual 112.68 119.02 -6.34 1.33e+00 5.65e-01 2.27e+01 angle pdb=" N GLY B 188 " pdb=" CA GLY B 188 " pdb=" C GLY B 188 " ideal model delta sigma weight residual 112.73 118.17 -5.44 1.20e+00 6.94e-01 2.06e+01 angle pdb=" C LYS B 482 " pdb=" N PRO B 483 " pdb=" CA PRO B 483 " ideal model delta sigma weight residual 119.05 114.40 4.65 1.11e+00 8.12e-01 1.75e+01 ... (remaining 6162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 2477 16.84 - 33.67: 216 33.67 - 50.51: 38 50.51 - 67.34: 5 67.34 - 84.18: 3 Dihedral angle restraints: 2739 sinusoidal: 986 harmonic: 1753 Sorted by residual: dihedral pdb=" C TPO B 473 " pdb=" N TPO B 473 " pdb=" CA TPO B 473 " pdb=" CB TPO B 473 " ideal model delta harmonic sigma weight residual -122.60 -113.34 -9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CB GLU B 223 " pdb=" CG GLU B 223 " pdb=" CD GLU B 223 " pdb=" OE1 GLU B 223 " ideal model delta sinusoidal sigma weight residual 0.00 84.18 -84.18 1 3.00e+01 1.11e-03 9.59e+00 dihedral pdb=" CB LYS B 273 " pdb=" CG LYS B 273 " pdb=" CD LYS B 273 " pdb=" CE LYS B 273 " ideal model delta sinusoidal sigma weight residual -60.00 -114.69 54.69 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 2736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 511 0.040 - 0.079: 197 0.079 - 0.119: 33 0.119 - 0.158: 11 0.158 - 0.198: 4 Chirality restraints: 756 Sorted by residual: chirality pdb=" CA TYR B 442 " pdb=" N TYR B 442 " pdb=" C TYR B 442 " pdb=" CB TYR B 442 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CB VAL B 83 " pdb=" CA VAL B 83 " pdb=" CG1 VAL B 83 " pdb=" CG2 VAL B 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA TPO B 473 " pdb=" N TPO B 473 " pdb=" C TPO B 473 " pdb=" CB TPO B 473 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 753 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 478 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C TYR B 478 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR B 478 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS B 479 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 81 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO B 82 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 347 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 348 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 348 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 348 " -0.020 5.00e-02 4.00e+02 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1688 2.90 - 3.40: 4128 3.40 - 3.90: 6539 3.90 - 4.40: 6902 4.40 - 4.90: 12571 Nonbonded interactions: 31828 Sorted by model distance: nonbonded pdb=" OD1 ASP B 206 " pdb=" N GLU B 207 " model vdw 2.403 3.120 nonbonded pdb=" O LEU A 259 " pdb=" OG SER A 262 " model vdw 2.431 3.040 nonbonded pdb=" OE1 GLN A 281 " pdb=" NZ LYS A 325 " model vdw 2.449 3.120 nonbonded pdb=" O LEU B 300 " pdb=" OG1 THR B 301 " model vdw 2.459 3.040 nonbonded pdb=" N GLU B 185 " pdb=" O GLU B 185 " model vdw 2.473 2.496 ... (remaining 31823 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: 0.730 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.350 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.007 0.134 4538 Z= 0.442 Angle : 0.704 9.354 6167 Z= 0.416 Chirality : 0.044 0.198 756 Planarity : 0.004 0.046 771 Dihedral : 13.199 84.180 1591 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.35), residues: 573 helix: 1.29 (0.28), residues: 348 sheet: 1.88 (0.99), residues: 28 loop : -1.14 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 268 HIS 0.007 0.001 HIS A 344 PHE 0.017 0.002 PHE B 163 TYR 0.008 0.001 TYR B 208 ARG 0.003 0.001 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.494 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1646 time to fit residues: 12.5392 Evaluate side-chains 46 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.129134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095517 restraints weight = 5541.725| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.38 r_work: 0.2911 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4538 Z= 0.208 Angle : 0.479 6.666 6167 Z= 0.251 Chirality : 0.038 0.126 756 Planarity : 0.004 0.044 771 Dihedral : 3.828 22.332 639 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.23 % Allowed : 6.55 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.37), residues: 573 helix: 1.79 (0.29), residues: 357 sheet: 1.09 (0.97), residues: 32 loop : -1.18 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS B 491 PHE 0.012 0.001 PHE B 163 TYR 0.004 0.001 TYR B 184 ARG 0.002 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.512 Fit side-chains REVERT: B 339 MET cc_start: 0.8588 (mmt) cc_final: 0.8308 (mmt) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.1718 time to fit residues: 11.1186 Evaluate side-chains 44 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.129047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093483 restraints weight = 5660.185| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.50 r_work: 0.2880 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4538 Z= 0.295 Angle : 0.503 5.699 6167 Z= 0.263 Chirality : 0.040 0.126 756 Planarity : 0.004 0.046 771 Dihedral : 3.781 18.919 639 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 9.71 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.37), residues: 573 helix: 1.74 (0.29), residues: 361 sheet: 1.91 (1.02), residues: 28 loop : -1.24 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.006 0.001 HIS A 344 PHE 0.015 0.002 PHE B 163 TYR 0.006 0.001 TYR B 208 ARG 0.002 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.520 Fit side-chains REVERT: B 129 GLN cc_start: 0.8614 (tp40) cc_final: 0.8193 (tt0) outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.1537 time to fit residues: 9.2028 Evaluate side-chains 40 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.130953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096835 restraints weight = 5676.959| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.42 r_work: 0.2927 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4538 Z= 0.136 Angle : 0.408 5.198 6167 Z= 0.215 Chirality : 0.036 0.126 756 Planarity : 0.003 0.040 771 Dihedral : 3.450 16.080 639 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.68 % Allowed : 11.06 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.37), residues: 573 helix: 2.00 (0.29), residues: 356 sheet: 1.37 (0.97), residues: 32 loop : -1.13 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 264 HIS 0.003 0.001 HIS A 344 PHE 0.009 0.001 PHE B 163 TYR 0.005 0.001 TYR B 442 ARG 0.001 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.600 Fit side-chains REVERT: B 129 GLN cc_start: 0.8469 (tp40) cc_final: 0.8046 (tt0) REVERT: B 154 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7874 (ttm110) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1581 time to fit residues: 9.8224 Evaluate side-chains 42 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.128456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.094079 restraints weight = 5718.889| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.45 r_work: 0.2883 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4538 Z= 0.213 Angle : 0.440 5.388 6167 Z= 0.229 Chirality : 0.038 0.125 756 Planarity : 0.004 0.041 771 Dihedral : 3.460 16.855 639 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.58 % Allowed : 11.06 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.37), residues: 573 helix: 1.96 (0.29), residues: 357 sheet: 1.36 (0.98), residues: 32 loop : -1.18 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 344 PHE 0.013 0.001 PHE B 163 TYR 0.007 0.001 TYR B 442 ARG 0.001 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.541 Fit side-chains REVERT: B 129 GLN cc_start: 0.8541 (tp40) cc_final: 0.8104 (tt0) REVERT: B 154 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7985 (ttm110) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.1534 time to fit residues: 9.7578 Evaluate side-chains 42 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.0040 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.132654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098450 restraints weight = 5636.100| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.44 r_work: 0.2950 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4538 Z= 0.110 Angle : 0.399 6.665 6167 Z= 0.204 Chirality : 0.036 0.126 756 Planarity : 0.003 0.038 771 Dihedral : 3.234 13.968 639 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.68 % Allowed : 13.32 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.37), residues: 573 helix: 2.15 (0.29), residues: 357 sheet: 1.07 (1.06), residues: 28 loop : -1.10 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 466 HIS 0.002 0.001 HIS B 491 PHE 0.009 0.001 PHE B 163 TYR 0.004 0.001 TYR B 442 ARG 0.001 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.554 Fit side-chains REVERT: B 129 GLN cc_start: 0.8441 (tp40) cc_final: 0.7989 (tt0) REVERT: B 154 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7866 (ttm110) outliers start: 3 outliers final: 2 residues processed: 45 average time/residue: 0.1652 time to fit residues: 10.0882 Evaluate side-chains 43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.129354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093218 restraints weight = 5693.475| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.51 r_work: 0.2852 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4538 Z= 0.354 Angle : 0.518 6.282 6167 Z= 0.266 Chirality : 0.041 0.127 756 Planarity : 0.004 0.043 771 Dihedral : 3.648 18.316 639 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.13 % Allowed : 13.09 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.37), residues: 573 helix: 1.75 (0.28), residues: 361 sheet: 1.98 (1.05), residues: 28 loop : -1.23 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.005 0.001 HIS A 344 PHE 0.019 0.002 PHE B 163 TYR 0.009 0.001 TYR B 442 ARG 0.002 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.505 Fit side-chains REVERT: B 129 GLN cc_start: 0.8660 (tp40) cc_final: 0.8233 (tt0) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.1500 time to fit residues: 9.4892 Evaluate side-chains 44 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.133301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.096942 restraints weight = 5628.207| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.52 r_work: 0.2905 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4538 Z= 0.155 Angle : 0.425 6.237 6167 Z= 0.219 Chirality : 0.037 0.125 756 Planarity : 0.003 0.041 771 Dihedral : 3.435 16.186 639 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.45 % Allowed : 14.45 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.37), residues: 573 helix: 1.99 (0.29), residues: 357 sheet: 1.16 (1.07), residues: 28 loop : -1.20 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 466 HIS 0.003 0.001 HIS A 344 PHE 0.010 0.001 PHE B 163 TYR 0.005 0.001 TYR B 184 ARG 0.001 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.558 Fit side-chains REVERT: B 129 GLN cc_start: 0.8514 (tp40) cc_final: 0.8067 (tt0) REVERT: B 154 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7887 (ttm110) outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.1630 time to fit residues: 9.8949 Evaluate side-chains 42 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.132275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095936 restraints weight = 5677.526| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.53 r_work: 0.2890 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4538 Z= 0.209 Angle : 0.442 6.133 6167 Z= 0.227 Chirality : 0.038 0.125 756 Planarity : 0.004 0.043 771 Dihedral : 3.441 16.295 639 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.68 % Allowed : 14.22 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.37), residues: 573 helix: 1.91 (0.29), residues: 359 sheet: 1.31 (0.94), residues: 32 loop : -1.18 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 264 HIS 0.004 0.001 HIS A 344 PHE 0.013 0.001 PHE B 163 TYR 0.005 0.001 TYR B 442 ARG 0.001 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.539 Fit side-chains REVERT: B 129 GLN cc_start: 0.8566 (tp40) cc_final: 0.7721 (tm-30) REVERT: B 154 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7910 (ttm110) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.1556 time to fit residues: 8.9708 Evaluate side-chains 43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.0020 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.133021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.096716 restraints weight = 5671.471| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.53 r_work: 0.2899 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4538 Z= 0.185 Angle : 0.428 6.056 6167 Z= 0.220 Chirality : 0.037 0.126 756 Planarity : 0.003 0.042 771 Dihedral : 3.387 15.510 639 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.68 % Allowed : 14.22 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.37), residues: 573 helix: 1.96 (0.29), residues: 359 sheet: 1.12 (1.06), residues: 28 loop : -1.18 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 264 HIS 0.004 0.001 HIS A 344 PHE 0.012 0.001 PHE B 163 TYR 0.005 0.001 TYR B 442 ARG 0.001 0.000 ARG B 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.492 Fit side-chains REVERT: B 129 GLN cc_start: 0.8531 (tp40) cc_final: 0.7689 (tm-30) REVERT: B 154 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7855 (ttm110) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.1510 time to fit residues: 9.1822 Evaluate side-chains 44 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.131646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097478 restraints weight = 5686.710| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.42 r_work: 0.2937 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4538 Z= 0.125 Angle : 0.405 5.903 6167 Z= 0.204 Chirality : 0.036 0.136 756 Planarity : 0.003 0.041 771 Dihedral : 3.212 12.327 639 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.68 % Allowed : 14.45 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.37), residues: 573 helix: 2.11 (0.29), residues: 359 sheet: 1.19 (1.05), residues: 28 loop : -1.14 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 264 HIS 0.002 0.001 HIS A 344 PHE 0.009 0.001 PHE B 163 TYR 0.003 0.001 TYR A 233 ARG 0.001 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.26 seconds wall clock time: 36 minutes 5.94 seconds (2165.94 seconds total)