Starting phenix.real_space_refine on Mon Sep 23 18:55:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/09_2024/8el7_28223.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/09_2024/8el7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/09_2024/8el7_28223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/09_2024/8el7_28223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/09_2024/8el7_28223.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/09_2024/8el7_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-5461/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: 4.38, per 1000 atoms: 0.96 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: 1.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.47 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: 1.15 Time building geometry restraints manager: 1.23 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: 0.780 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.130 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:14.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.529 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: 1.4244 time to fit residues: 85.5894 Evaluate side-chains 46 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.539 Fit side-chains REVERT: B 181 GLN cc_start: 0.7681 (mt0) cc_final: 0.7475 (mt0) REVERT: B 335 ASN cc_start: 0.7739 (t0) cc_final: 0.7375 (t0) REVERT: B 372 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6908 (mp0) outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 1.3821 time to fit residues: 64.6767 Evaluate side-chains 43 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 29 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4632 Z= 0.213 Angle : 0.511 5.039 6295 Z= 0.263 Chirality : 0.040 0.133 771 Planarity : 0.004 0.037 789 Dihedral : 3.556 12.426 653 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 7.16 % Favored : 90.89 % 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: 1.31 (0.35), residues: 582 helix: 1.89 (0.28), residues: 358 sheet: 0.72 (0.95), residues: 32 loop : -1.09 (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 0.017 0.002 PHE B 163 TYR 0.007 0.001 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 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.513 Fit side-chains REVERT: A 333 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.4685 (ptp90) REVERT: B 335 ASN cc_start: 0.7789 (t0) cc_final: 0.7375 (t0) REVERT: B 372 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6752 (mp0) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 1.6502 time to fit residues: 78.4149 Evaluate side-chains 44 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL 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 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1283 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= 0.190 Angle : 0.488 5.038 6295 Z= 0.250 Chirality : 0.039 0.131 771 Planarity : 0.004 0.036 789 Dihedral : 3.485 12.298 653 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.17 % Allowed : 8.89 % 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: 1.39 (0.35), residues: 582 helix: 1.96 (0.28), residues: 358 sheet: 0.76 (0.94), residues: 32 loop : -1.07 (0.43), residues: 192 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 0.016 0.002 PHE B 163 TYR 0.007 0.001 TYR B 334 ARG 0.001 0.000 ARG B 352 *********************** 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 51 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.629 Fit side-chains REVERT: A 333 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.4681 (ptp90) REVERT: B 150 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6797 (mtmm) REVERT: B 335 ASN cc_start: 0.7800 (t0) cc_final: 0.7369 (t0) REVERT: B 372 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6747 (mp0) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 1.5658 time to fit residues: 76.0870 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 4632 Z= 0.100 Angle : 0.392 5.014 6295 Z= 0.202 Chirality : 0.036 0.126 771 Planarity : 0.003 0.033 789 Dihedral : 3.138 15.941 653 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.30 % Allowed : 10.20 % Favored : 88.50 % 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: 1.78 (0.36), residues: 582 helix: 2.23 (0.28), residues: 366 sheet: 0.88 (0.95), residues: 32 loop : -0.97 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 204 HIS 0.008 0.001 HIS B 491 PHE 0.016 0.001 PHE A 232 TYR 0.004 0.001 TYR B 445 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 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.511 Fit side-chains REVERT: A 330 GLU cc_start: 0.7698 (mm-30) cc_final: 0.6983 (mm-30) REVERT: A 333 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.4542 (ptp90) REVERT: B 150 LYS cc_start: 0.6727 (mtpp) cc_final: 0.6358 (mtmm) REVERT: B 335 ASN cc_start: 0.7772 (t0) cc_final: 0.7365 (t0) REVERT: B 372 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6670 (mp0) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 1.4523 time to fit residues: 69.3254 Evaluate side-chains 40 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 180 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.0270 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.7842 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4632 Z= 0.242 Angle : 0.517 5.172 6295 Z= 0.264 Chirality : 0.041 0.133 771 Planarity : 0.004 0.036 789 Dihedral : 3.523 14.046 653 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.74 % Allowed : 10.41 % Favored : 87.85 % 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: 1.49 (0.36), residues: 582 helix: 2.05 (0.28), residues: 358 sheet: 0.82 (0.95), residues: 32 loop : -1.08 (0.43), residues: 192 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 0.024 0.002 PHE A 232 TYR 0.008 0.002 TYR B 334 ARG 0.002 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 46 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.511 Fit side-chains REVERT: A 333 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.4671 (ptp90) REVERT: B 150 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6672 (mtmm) REVERT: B 335 ASN cc_start: 0.7883 (t0) cc_final: 0.7435 (t0) REVERT: B 372 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6767 (mp0) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 1.6862 time to fit residues: 76.6615 Evaluate side-chains 45 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 35 optimal weight: 0.0050 chunk 34 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4632 Z= 0.162 Angle : 0.455 5.021 6295 Z= 0.234 Chirality : 0.038 0.129 771 Planarity : 0.003 0.034 789 Dihedral : 3.435 17.738 653 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.74 % Allowed : 10.41 % Favored : 87.85 % 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 (0.36), residues: 582 helix: 2.18 (0.28), residues: 357 sheet: 0.85 (0.96), residues: 32 loop : -1.10 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 263 HIS 0.009 0.001 HIS B 491 PHE 0.021 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG B 352 *********************** 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 46 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.523 Fit side-chains REVERT: A 333 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.4563 (ptp90) REVERT: B 150 LYS cc_start: 0.6969 (mtpp) cc_final: 0.6605 (mtmm) REVERT: B 335 ASN cc_start: 0.7863 (t0) cc_final: 0.7423 (t0) REVERT: B 372 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6768 (mp0) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 1.6672 time to fit residues: 75.7852 Evaluate side-chains 45 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4632 Z= 0.185 Angle : 0.471 5.016 6295 Z= 0.242 Chirality : 0.039 0.129 771 Planarity : 0.004 0.035 789 Dihedral : 3.498 19.541 653 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.74 % Allowed : 10.85 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.35), residues: 582 helix: 2.11 (0.28), residues: 358 sheet: 0.83 (0.96), residues: 32 loop : -1.11 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 263 HIS 0.010 0.001 HIS B 491 PHE 0.021 0.002 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 46 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.641 Fit side-chains REVERT: A 333 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.4543 (ptp90) REVERT: B 150 LYS cc_start: 0.6972 (mtpp) cc_final: 0.6641 (mtmm) REVERT: B 335 ASN cc_start: 0.7892 (t0) cc_final: 0.7445 (t0) REVERT: B 372 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6760 (mp0) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 1.7743 time to fit residues: 80.5868 Evaluate side-chains 45 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 56 optimal weight: 0.0770 chunk 26 optimal weight: 0.3980 chunk 38 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 0.018 4632 Z= 0.148 Angle : 0.437 5.014 6295 Z= 0.226 Chirality : 0.038 0.128 771 Planarity : 0.003 0.034 789 Dihedral : 3.400 21.763 653 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.17 % Allowed : 10.20 % Favored : 87.64 % 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: 1.70 (0.36), residues: 582 helix: 2.24 (0.28), residues: 358 sheet: 0.87 (0.96), residues: 32 loop : -1.04 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 263 HIS 0.010 0.001 HIS B 491 PHE 0.020 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 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.552 Fit side-chains REVERT: A 333 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.4549 (ptp90) REVERT: B 335 ASN cc_start: 0.7852 (t0) cc_final: 0.7401 (t0) REVERT: B 372 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6648 (mp0) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 1.6359 time to fit residues: 77.7354 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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 180 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1456 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= 0.223 Angle : 0.511 5.061 6295 Z= 0.261 Chirality : 0.040 0.131 771 Planarity : 0.004 0.035 789 Dihedral : 3.573 21.919 653 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 11.28 % Favored : 86.77 % 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: 1.46 (0.35), residues: 582 helix: 2.04 (0.28), residues: 359 sheet: 0.77 (0.95), residues: 32 loop : -1.12 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 263 HIS 0.010 0.002 HIS B 491 PHE 0.022 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 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.517 Fit side-chains REVERT: A 333 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.4639 (ptp90) REVERT: B 150 LYS cc_start: 0.7116 (mtpp) cc_final: 0.6816 (mtmm) REVERT: B 335 ASN cc_start: 0.7906 (t0) cc_final: 0.7455 (t0) REVERT: B 372 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6766 (mp0) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 1.6591 time to fit residues: 75.3722 Evaluate side-chains 46 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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 Chi-restraints excluded: chain B residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.138531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.103180 restraints weight = 14514.415| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.27 r_work: 0.3029 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1423 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= 0.158 Angle : 0.457 5.003 6295 Z= 0.235 Chirality : 0.038 0.128 771 Planarity : 0.003 0.034 789 Dihedral : 3.484 23.632 653 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.95 % Allowed : 11.50 % Favored : 86.55 % 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: 1.63 (0.36), residues: 582 helix: 2.21 (0.28), residues: 357 sheet: 0.87 (0.97), residues: 32 loop : -1.12 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 263 HIS 0.009 0.001 HIS B 491 PHE 0.020 0.001 PHE A 232 TYR 0.007 0.001 TYR B 184 ARG 0.001 0.000 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1861.20 seconds wall clock time: 33 minutes 22.02 seconds (2002.02 seconds total)