Starting phenix.real_space_refine on Tue Feb 11 07:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8el7_28223/02_2025/8el7_28223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8el7_28223/02_2025/8el7_28223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8el7_28223/02_2025/8el7_28223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8el7_28223/02_2025/8el7_28223.map" model { file = "/net/cci-nas-00/data/ceres_data/8el7_28223/02_2025/8el7_28223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8el7_28223/02_2025/8el7_28223.cif" } resolution = 2.8 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= 0.198 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 2921 2.51 5 N 802 2.21 5 O 810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 4562 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1134 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Conformer: "B" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 1130 Conformer: "C" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 1130 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3423 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 15, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 19, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 4.09, per 1000 atoms: 0.90 Number of scatterers: 4562 At special positions: 0 Unit cell: (54.5344, 80.0974, 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 810 8.00 N 802 7.00 C 2921 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: 1.20 Conformation dependent library (CDL) restraints added in 814.1 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 1 sheets defined 67.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.652A pdb=" N ALA A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.517A pdb=" N LEU A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 269 " --> pdb=" O ARG A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 269' Processing helix chain 'A' and resid 279 through 290 removed outlier: 3.762A pdb=" N GLY A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.720A pdb=" N THR A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 14 through 29 removed outlier: 4.129A pdb=" N ILE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 19 " --> pdb=" O ALA B 15 " (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 56 removed outlier: 3.512A pdb=" N PHE B 51 " --> pdb=" O CYS B 47 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 Processing helix chain 'B' and resid 85 through 96 removed outlier: 3.678A pdb=" N MET B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 128 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.597A pdb=" N GLN B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.837A 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 184 Processing helix chain 'B' and resid 187 through 201 removed outlier: 4.103A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 238 removed outlier: 3.535A pdb=" N ASN B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 270 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 297 removed outlier: 4.747A pdb=" N ASP B 294 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 295 " --> pdb=" O CYS B 292 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 297 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.691A pdb=" N HIS B 343 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 355 " --> pdb=" O LYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 377 removed outlier: 4.050A pdb=" N THR B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Proline residue: B 365 - end of helix removed outlier: 3.579A pdb=" N ALA B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 389 removed outlier: 3.787A pdb=" N ARG B 381 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 387 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 412 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 417 through 432 removed outlier: 3.618A pdb=" N LYS B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 removed outlier: 3.639A pdb=" N TYR B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.217A pdb=" N ILE A 230 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 276 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE A 232 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASN A 278 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 234 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 273 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N HIS A 348 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 275 " --> pdb=" O HIS A 348 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 710 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: 1.05 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: 1.19 - 1.31: 728 1.31 - 1.44: 1153 1.44 - 1.56: 2711 1.56 - 1.68: 2 1.68 - 1.81: 38 Bond restraints: 4632 Sorted by residual: bond pdb=" O3P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.477 0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C ARG A 375 " pdb=" CA BARG A 375 " ideal model delta sigma weight residual 1.522 1.430 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" C ARG A 375 " pdb=" CA CARG A 375 " ideal model delta sigma weight residual 1.522 1.430 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" O1P 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 4.22e+01 bond pdb=" O2P 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 4.16e+01 ... (remaining 4627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 6104 1.52 - 3.03: 145 3.03 - 4.55: 33 4.55 - 6.06: 10 6.06 - 7.58: 3 Bond angle restraints: 6295 Sorted by residual: angle pdb=" N GLU B 4 " pdb=" CA GLU B 4 " pdb=" C GLU B 4 " ideal model delta sigma weight residual 111.28 115.77 -4.49 1.09e+00 8.42e-01 1.70e+01 angle pdb=" C TRP B 466 " pdb=" N TYR B 467 " pdb=" CA TYR B 467 " ideal model delta sigma weight residual 121.70 114.71 6.99 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CA TRP B 466 " pdb=" C TRP B 466 " pdb=" N TYR B 467 " ideal model delta sigma weight residual 116.02 121.32 -5.30 1.42e+00 4.96e-01 1.39e+01 angle pdb=" N ALA B 15 " pdb=" CA ALA B 15 " pdb=" C ALA B 15 " ideal model delta sigma weight residual 113.38 117.91 -4.53 1.23e+00 6.61e-01 1.35e+01 angle pdb=" N GLY B 13 " pdb=" CA GLY B 13 " pdb=" C GLY B 13 " ideal model delta sigma weight residual 112.73 116.85 -4.12 1.20e+00 6.94e-01 1.18e+01 ... (remaining 6290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 2582 17.32 - 34.64: 188 34.64 - 51.96: 31 51.96 - 69.28: 6 69.28 - 86.60: 5 Dihedral angle restraints: 2812 sinusoidal: 1029 harmonic: 1783 Sorted by residual: dihedral pdb=" CA GLY B 13 " pdb=" C GLY B 13 " pdb=" N GLU B 14 " pdb=" CA GLU B 14 " ideal model delta harmonic sigma weight residual 180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 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 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" N TRP B 466 " pdb=" C TRP B 466 " pdb=" CA TRP B 466 " pdb=" CB TRP B 466 " ideal model delta harmonic sigma weight residual 122.80 114.49 8.31 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 2809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 541 0.038 - 0.077: 177 0.077 - 0.115: 39 0.115 - 0.154: 10 0.154 - 0.192: 4 Chirality restraints: 771 Sorted by residual: chirality pdb=" CA ALA B 15 " pdb=" N ALA B 15 " pdb=" C ALA B 15 " pdb=" CB ALA B 15 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CA BARG A 375 " pdb=" N ARG A 375 " pdb=" C ARG A 375 " pdb=" CB BARG A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA CARG A 375 " pdb=" N ARG A 375 " pdb=" C ARG A 375 " pdb=" CB CARG A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 768 not shown) Planarity restraints: 789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 463 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C GLY B 463 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY B 463 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP B 464 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 5 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C ARG B 5 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG B 5 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA B 6 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 478 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C TYR B 478 " 0.020 2.00e-02 2.50e+03 pdb=" O TYR B 478 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS B 479 " -0.007 2.00e-02 2.50e+03 ... (remaining 786 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1226 2.82 - 3.34: 4034 3.34 - 3.86: 6742 3.86 - 4.38: 7705 4.38 - 4.90: 14105 Nonbonded interactions: 33812 Sorted by model distance: nonbonded pdb=" O LEU B 80 " pdb=" OG1 THR B 84 " model vdw 2.295 3.040 nonbonded pdb=" O LEU B 70 " pdb=" OG SER B 74 " model vdw 2.311 3.040 nonbonded pdb=" N GLU B 3 " pdb=" OE1 GLU B 3 " model vdw 2.356 3.120 nonbonded pdb=" O PRO B 399 " pdb=" ND2 ASN B 407 " model vdw 2.374 3.120 nonbonded pdb=" N ASP B 464 " pdb=" OD1 ASP B 464 " model vdw 2.407 3.120 ... (remaining 33807 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=0.25 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: 0.770 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.710 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.006 0.133 4632 Z= 0.392 Angle : 0.611 7.578 6295 Z= 0.356 Chirality : 0.042 0.192 771 Planarity : 0.004 0.028 789 Dihedral : 13.128 86.604 1644 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.35), residues: 582 helix: 1.64 (0.28), residues: 355 sheet: 0.82 (0.97), residues: 32 loop : -1.30 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 466 HIS 0.003 0.001 HIS B 262 PHE 0.012 0.001 PHE B 163 TYR 0.009 0.001 TYR B 334 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.521 Fit side-chains REVERT: B 181 GLN cc_start: 0.7585 (mt0) cc_final: 0.7336 (mt0) REVERT: B 335 ASN cc_start: 0.7658 (t0) cc_final: 0.7363 (t0) REVERT: B 372 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6962 (mp0) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.4128 time to fit residues: 84.9300 Evaluate side-chains 46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 0.1980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.097685 restraints weight = 19671.965| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.09 r_work: 0.2935 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4632 Z= 0.161 Angle : 0.484 5.754 6295 Z= 0.249 Chirality : 0.039 0.134 771 Planarity : 0.004 0.036 789 Dihedral : 3.496 12.768 653 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.30 % Allowed : 6.07 % Favored : 92.62 % 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: 1.17 (0.36), residues: 582 helix: 1.76 (0.28), residues: 368 sheet: 0.70 (0.96), residues: 32 loop : -1.31 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 466 HIS 0.005 0.001 HIS A 343 PHE 0.014 0.001 PHE B 163 TYR 0.006 0.001 TYR A 344 ARG 0.001 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.550 Fit side-chains REVERT: B 335 ASN cc_start: 0.7845 (t0) cc_final: 0.7481 (t0) REVERT: B 372 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7209 (mp0) outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 1.5079 time to fit residues: 70.6853 Evaluate side-chains 43 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.100281 restraints weight = 24526.713| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.21 r_work: 0.2901 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4632 Z= 0.236 Angle : 0.532 5.054 6295 Z= 0.273 Chirality : 0.041 0.134 771 Planarity : 0.004 0.037 789 Dihedral : 3.641 12.774 653 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.17 % Allowed : 6.72 % Favored : 91.11 % 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: 1.23 (0.35), residues: 582 helix: 1.82 (0.28), residues: 358 sheet: 0.69 (0.94), residues: 32 loop : -1.12 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 263 HIS 0.008 0.002 HIS A 343 PHE 0.018 0.002 PHE B 163 TYR 0.008 0.002 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.551 Fit side-chains REVERT: A 333 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.4777 (ptp90) REVERT: B 335 ASN cc_start: 0.7827 (t0) cc_final: 0.7397 (t0) REVERT: B 372 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6773 (mp0) outliers start: 10 outliers final: 5 residues processed: 46 average time/residue: 1.7630 time to fit residues: 83.7354 Evaluate side-chains 45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.0270 chunk 43 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104634 restraints weight = 18907.723| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 4.43 r_work: 0.2866 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4632 Z= 0.181 Angle : 0.477 5.033 6295 Z= 0.245 Chirality : 0.039 0.131 771 Planarity : 0.004 0.036 789 Dihedral : 3.479 12.388 653 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.95 % Allowed : 9.11 % Favored : 88.94 % 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 (0.35), residues: 582 helix: 1.98 (0.28), residues: 358 sheet: 0.75 (0.94), residues: 32 loop : -1.09 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 263 HIS 0.009 0.001 HIS B 491 PHE 0.016 0.001 PHE B 163 TYR 0.007 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.516 Fit side-chains REVERT: A 333 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.4832 (ptp90) REVERT: B 150 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6578 (mtmm) REVERT: B 335 ASN cc_start: 0.7861 (t0) cc_final: 0.7433 (t0) REVERT: B 372 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6878 (mp0) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 1.6733 time to fit residues: 81.2078 Evaluate side-chains 46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109081 restraints weight = 19251.166| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 4.50 r_work: 0.3036 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4632 Z= 0.117 Angle : 0.413 5.010 6295 Z= 0.213 Chirality : 0.037 0.128 771 Planarity : 0.003 0.034 789 Dihedral : 3.261 15.353 653 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.95 % Allowed : 9.98 % Favored : 88.07 % 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: 1.54 (0.36), residues: 582 helix: 2.04 (0.28), residues: 369 sheet: 0.85 (0.95), residues: 32 loop : -1.17 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 263 HIS 0.008 0.001 HIS B 491 PHE 0.014 0.001 PHE A 232 TYR 0.005 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.532 Fit side-chains REVERT: A 333 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.4741 (ptp90) REVERT: B 150 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6520 (mtmm) REVERT: B 335 ASN cc_start: 0.7888 (t0) cc_final: 0.7476 (t0) REVERT: B 372 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6960 (mp0) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 1.6210 time to fit residues: 77.0446 Evaluate side-chains 46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.0010 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102926 restraints weight = 20205.653| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.80 r_work: 0.2902 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4632 Z= 0.142 Angle : 0.432 5.002 6295 Z= 0.223 Chirality : 0.038 0.128 771 Planarity : 0.003 0.035 789 Dihedral : 3.257 15.563 653 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.52 % Allowed : 10.41 % Favored : 88.07 % 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: 1.76 (0.36), residues: 582 helix: 2.28 (0.28), residues: 358 sheet: 0.88 (0.96), residues: 32 loop : -0.99 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 263 HIS 0.008 0.001 HIS B 491 PHE 0.015 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.479 Fit side-chains REVERT: A 333 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.4630 (ptp90) REVERT: B 335 ASN cc_start: 0.7855 (t0) cc_final: 0.7416 (t0) REVERT: B 372 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6829 (mp0) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 1.7694 time to fit residues: 78.5095 Evaluate side-chains 43 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 5.9990 chunk 56 optimal weight: 0.0020 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.0570 chunk 57 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103321 restraints weight = 21086.820| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.89 r_work: 0.3004 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4632 Z= 0.129 Angle : 0.417 5.003 6295 Z= 0.215 Chirality : 0.037 0.126 771 Planarity : 0.003 0.034 789 Dihedral : 3.200 17.737 653 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.95 % Allowed : 9.76 % Favored : 88.29 % 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: 1.96 (0.36), residues: 582 helix: 2.42 (0.28), residues: 353 sheet: 0.90 (0.96), residues: 32 loop : -0.77 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 263 HIS 0.008 0.001 HIS B 491 PHE 0.015 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.486 Fit side-chains REVERT: A 333 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.4767 (ptp90) REVERT: B 150 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6612 (mtmm) REVERT: B 335 ASN cc_start: 0.7883 (t0) cc_final: 0.7473 (t0) REVERT: B 372 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6849 (mp0) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 1.6532 time to fit residues: 80.2353 Evaluate side-chains 45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.103168 restraints weight = 17517.155| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.58 r_work: 0.2919 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4632 Z= 0.138 Angle : 0.425 5.000 6295 Z= 0.219 Chirality : 0.038 0.128 771 Planarity : 0.003 0.034 789 Dihedral : 3.243 18.567 653 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.74 % Allowed : 9.98 % Favored : 88.29 % 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: 1.93 (0.36), residues: 582 helix: 2.42 (0.28), residues: 352 sheet: 0.91 (0.96), residues: 32 loop : -0.82 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 263 HIS 0.009 0.001 HIS B 491 PHE 0.017 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.468 Fit side-chains REVERT: A 333 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.4717 (ptp90) REVERT: B 335 ASN cc_start: 0.7892 (t0) cc_final: 0.7464 (t0) REVERT: B 372 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6832 (mp0) outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 1.7583 time to fit residues: 77.9697 Evaluate side-chains 43 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102802 restraints weight = 20131.819| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.80 r_work: 0.2912 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4632 Z= 0.137 Angle : 0.424 5.004 6295 Z= 0.218 Chirality : 0.038 0.127 771 Planarity : 0.003 0.034 789 Dihedral : 3.256 19.839 653 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.74 % Allowed : 10.20 % Favored : 88.07 % 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: 1.94 (0.36), residues: 582 helix: 2.43 (0.28), residues: 352 sheet: 0.92 (0.96), residues: 32 loop : -0.82 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 263 HIS 0.009 0.001 HIS B 491 PHE 0.018 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.492 Fit side-chains REVERT: A 333 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.4708 (ptp90) REVERT: B 150 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6525 (mtmm) REVERT: B 335 ASN cc_start: 0.7896 (t0) cc_final: 0.7481 (t0) REVERT: B 372 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6825 (mp0) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 1.8629 time to fit residues: 84.4582 Evaluate side-chains 45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098724 restraints weight = 13689.991| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.69 r_work: 0.2848 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4632 Z= 0.221 Angle : 0.499 5.072 6295 Z= 0.255 Chirality : 0.040 0.130 771 Planarity : 0.004 0.035 789 Dihedral : 3.503 19.759 653 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 10.41 % Favored : 88.07 % 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: 1.52 (0.35), residues: 582 helix: 2.08 (0.28), residues: 359 sheet: 0.80 (0.95), residues: 32 loop : -1.09 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 263 HIS 0.009 0.002 HIS B 491 PHE 0.020 0.002 PHE A 232 TYR 0.008 0.002 TYR B 334 ARG 0.001 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.554 Fit side-chains REVERT: A 333 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.4752 (ptp90) REVERT: B 335 ASN cc_start: 0.7952 (t0) cc_final: 0.7496 (t0) REVERT: B 372 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6906 (mp0) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 1.8339 time to fit residues: 77.6217 Evaluate side-chains 42 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 0.0070 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.0040 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112875 restraints weight = 21723.988| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 5.45 r_work: 0.3031 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4632 Z= 0.111 Angle : 0.400 4.987 6295 Z= 0.207 Chirality : 0.037 0.125 771 Planarity : 0.003 0.034 789 Dihedral : 3.279 23.208 653 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.74 % Allowed : 10.20 % Favored : 88.07 % 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: 1.92 (0.36), residues: 582 helix: 2.45 (0.28), residues: 354 sheet: 0.94 (0.96), residues: 32 loop : -0.94 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 466 HIS 0.009 0.001 HIS B 491 PHE 0.016 0.001 PHE A 232 TYR 0.005 0.001 TYR A 344 ARG 0.001 0.000 ARG B 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.76 seconds wall clock time: 58 minutes 21.92 seconds (3501.92 seconds total)