Starting phenix.real_space_refine on Sat Apr 6 09:46:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/04_2024/8u1m_41817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/04_2024/8u1m_41817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/04_2024/8u1m_41817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/04_2024/8u1m_41817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/04_2024/8u1m_41817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/04_2024/8u1m_41817_updated.pdb" } resolution = 3.5 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= 0.002 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 4988 2.51 5 N 1318 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 420": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7882 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3789 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 10, 'TRANS': 452} Chain breaks: 2 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4029 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 11, 'TRANS': 482} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.69, per 1000 atoms: 0.60 Number of scatterers: 7882 At special positions: 0 Unit cell: (90.948, 110.682, 108.108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1540 8.00 N 1318 7.00 C 4988 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 - 3.50 Amino acid : False - 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: 3.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 5 sheets defined 35.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 removed outlier: 3.849A pdb=" N MET A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 60 removed outlier: 3.706A pdb=" N GLU A 42 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.790A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.570A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 397 through 420 removed outlier: 3.540A pdb=" N GLU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 442 removed outlier: 6.932A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.572A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 31 removed outlier: 4.353A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 59 removed outlier: 3.731A pdb=" N ARG B 41 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU B 42 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 59 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.633A pdb=" N TYR B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 138 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 397 through 420 removed outlier: 3.887A pdb=" N GLU B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 442 removed outlier: 6.599A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 497 through 505 removed outlier: 3.873A pdb=" N ARG B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG B 505 " --> pdb=" O ARG B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.690A pdb=" N VAL B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 166 through 169 removed outlier: 3.729A pdb=" N ARG A 168 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 147 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 143 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N HIS A 184 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL A 143 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 182 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 145 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS A 180 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 147 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLY A 178 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 179 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 85 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE A 75 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A 214 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR A 216 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.575A pdb=" N LEU A 354 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 378 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR A 355 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL A 380 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 316 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 73 through 77 removed outlier: 4.326A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 316 through 322 removed outlier: 4.413A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 320 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 377 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 484 through 486 removed outlier: 6.084A pdb=" N VAL B 510 " --> pdb=" O ILE B 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 262 hydrogen bonds defined for protein. 594 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: 2.02 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2483 1.34 - 1.45: 1081 1.45 - 1.57: 4405 1.57 - 1.69: 4 1.69 - 1.81: 48 Bond restraints: 8021 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.217 0.226 1.00e-02 1.00e+04 5.12e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.92e+02 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.370 0.053 1.10e-02 8.26e+03 2.36e+01 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.81e+01 bond pdb=" C1' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.416 1.361 0.055 1.30e-02 5.92e+03 1.79e+01 ... (remaining 8016 not shown) Histogram of bond angle deviations from ideal: 80.37 - 95.41: 7 95.41 - 110.46: 1868 110.46 - 125.50: 8835 125.50 - 140.54: 83 140.54 - 155.59: 2 Bond angle restraints: 10795 Sorted by residual: angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 155.59 -34.32 1.00e+00 1.00e+00 1.18e+03 angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.25 -33.98 1.00e+00 1.00e+00 1.15e+03 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 83.50 31.69 1.76e+00 3.23e-01 3.24e+02 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 84.32 30.87 1.76e+00 3.23e-01 3.08e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 140.19 -31.36 2.33e+00 1.85e-01 1.82e+02 ... (remaining 10790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4276 17.98 - 35.95: 516 35.95 - 53.93: 112 53.93 - 71.91: 22 71.91 - 89.88: 10 Dihedral angle restraints: 4936 sinusoidal: 2122 harmonic: 2814 Sorted by residual: dihedral pdb=" CA MET B 512 " pdb=" C MET B 512 " pdb=" N THR B 513 " pdb=" CA THR B 513 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA MET A 25 " pdb=" C MET A 25 " pdb=" N SER A 26 " pdb=" CA SER A 26 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR A 456 " pdb=" C TYR A 456 " pdb=" N HIS A 457 " pdb=" CA HIS A 457 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1117 0.094 - 0.188: 52 0.188 - 0.282: 4 0.282 - 0.376: 0 0.376 - 0.471: 2 Chirality restraints: 1175 Sorted by residual: chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.96 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.96 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1172 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 311 " -0.014 2.00e-02 2.50e+03 1.70e-02 7.19e+00 pdb=" CG TRP A 311 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 311 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 311 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 311 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 311 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 311 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 211 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 212 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " -0.136 9.50e-02 1.11e+02 6.11e-02 2.39e+00 pdb=" NE ARG A 177 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " -0.007 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 73 2.40 - 3.03: 4896 3.03 - 3.65: 13155 3.65 - 4.28: 19306 4.28 - 4.90: 29944 Nonbonded interactions: 67374 Sorted by model distance: nonbonded pdb=" CB SER B 159 " pdb=" CD1 PHE B 165 " model vdw 1.781 3.740 nonbonded pdb=" O2G ATP A 801 " pdb="MG MG A 802 " model vdw 1.938 2.170 nonbonded pdb=" O3A ATP B 801 " pdb="MG MG B 802 " model vdw 1.967 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.971 2.170 nonbonded pdb=" O2A ATP A 801 " pdb="MG MG A 802 " model vdw 2.028 2.170 ... (remaining 67369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 10 through 490 or resid 507 through 530 or resid 801 throu \ gh 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 3.830 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.630 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.005 0.226 8021 Z= 0.337 Angle : 1.167 34.316 10795 Z= 0.717 Chirality : 0.048 0.471 1175 Planarity : 0.004 0.061 1374 Dihedral : 16.519 89.885 3122 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.35 % Allowed : 18.79 % Favored : 80.86 % 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: -1.18 (0.27), residues: 947 helix: 0.01 (0.30), residues: 313 sheet: -1.23 (0.42), residues: 156 loop : -1.10 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 311 HIS 0.007 0.001 HIS A 314 PHE 0.010 0.001 PHE A 208 TYR 0.015 0.002 TYR A 372 ARG 0.006 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.5009 (mmt) cc_final: 0.4370 (mmt) REVERT: B 362 MET cc_start: 0.4810 (tpt) cc_final: 0.4181 (tpp) REVERT: B 475 MET cc_start: 0.4829 (mtm) cc_final: 0.4611 (ptp) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.2373 time to fit residues: 12.3490 Evaluate side-chains 31 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 6.9990 chunk 72 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 0.0570 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 446 ASN B 118 GLN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN B 406 ASN B 431 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8021 Z= 0.234 Angle : 0.597 7.016 10795 Z= 0.325 Chirality : 0.042 0.162 1175 Planarity : 0.004 0.057 1374 Dihedral : 10.354 80.504 1110 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.32 % Allowed : 18.33 % Favored : 79.35 % 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: -1.50 (0.26), residues: 947 helix: -0.30 (0.29), residues: 317 sheet: -1.40 (0.40), residues: 164 loop : -1.26 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 311 HIS 0.008 0.002 HIS A 314 PHE 0.008 0.001 PHE B 303 TYR 0.013 0.002 TYR B 519 ARG 0.006 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 32 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 167 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8792 (m) REVERT: B 362 MET cc_start: 0.5004 (tpt) cc_final: 0.4029 (tpp) outliers start: 20 outliers final: 11 residues processed: 49 average time/residue: 0.1843 time to fit residues: 13.7052 Evaluate side-chains 43 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8021 Z= 0.234 Angle : 0.589 6.895 10795 Z= 0.319 Chirality : 0.041 0.164 1175 Planarity : 0.004 0.058 1374 Dihedral : 10.364 89.158 1110 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.71 % Allowed : 18.33 % Favored : 77.96 % 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 (0.26), residues: 947 helix: -0.61 (0.28), residues: 321 sheet: -1.40 (0.41), residues: 163 loop : -1.31 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 311 HIS 0.007 0.001 HIS A 314 PHE 0.009 0.001 PHE B 303 TYR 0.012 0.002 TYR A 300 ARG 0.007 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 33 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8958 (ppp) cc_final: 0.8647 (ppp) REVERT: B 84 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6906 (t80) REVERT: B 93 MET cc_start: 0.5410 (mmt) cc_final: 0.5067 (mmt) REVERT: B 125 MET cc_start: 0.6603 (pmm) cc_final: 0.6397 (pmm) REVERT: B 156 MET cc_start: 0.4858 (tpp) cc_final: 0.4651 (mmm) REVERT: B 167 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8834 (m) REVERT: B 300 TYR cc_start: 0.2566 (OUTLIER) cc_final: 0.2268 (m-10) REVERT: B 362 MET cc_start: 0.4913 (tpt) cc_final: 0.4184 (tpp) outliers start: 32 outliers final: 14 residues processed: 62 average time/residue: 0.1920 time to fit residues: 17.1829 Evaluate side-chains 48 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 31 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 41 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 chunk 82 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8021 Z= 0.142 Angle : 0.539 7.942 10795 Z= 0.287 Chirality : 0.041 0.154 1175 Planarity : 0.004 0.036 1374 Dihedral : 9.892 88.500 1110 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.25 % Allowed : 18.21 % Favored : 78.54 % 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: -1.58 (0.27), residues: 947 helix: -0.42 (0.29), residues: 316 sheet: -1.40 (0.41), residues: 162 loop : -1.29 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 311 HIS 0.004 0.001 HIS A 457 PHE 0.015 0.001 PHE B 165 TYR 0.017 0.001 TYR A 372 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 31 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.5603 (mmt) cc_final: 0.5324 (mmt) REVERT: B 125 MET cc_start: 0.6763 (pmm) cc_final: 0.6506 (pmm) REVERT: B 156 MET cc_start: 0.4887 (tpp) cc_final: 0.4681 (mmm) REVERT: B 167 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8887 (m) REVERT: B 300 TYR cc_start: 0.2308 (OUTLIER) cc_final: 0.1784 (m-10) REVERT: B 362 MET cc_start: 0.4902 (tpt) cc_final: 0.3873 (tpp) REVERT: B 512 MET cc_start: 0.5049 (ppp) cc_final: 0.4270 (ppp) outliers start: 28 outliers final: 17 residues processed: 57 average time/residue: 0.1750 time to fit residues: 15.1205 Evaluate side-chains 49 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN B 118 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8021 Z= 0.329 Angle : 0.697 11.949 10795 Z= 0.363 Chirality : 0.043 0.161 1175 Planarity : 0.005 0.068 1374 Dihedral : 10.478 88.348 1110 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 33.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.29 % Allowed : 19.61 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.26), residues: 947 helix: -0.81 (0.28), residues: 314 sheet: -1.58 (0.40), residues: 164 loop : -1.39 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 311 HIS 0.007 0.002 HIS B 184 PHE 0.013 0.002 PHE A 84 TYR 0.018 0.002 TYR A 275 ARG 0.008 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 29 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8895 (ppp) cc_final: 0.8546 (ppp) REVERT: B 84 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7085 (t80) REVERT: B 125 MET cc_start: 0.6679 (pmm) cc_final: 0.6452 (pmm) REVERT: B 167 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8854 (m) REVERT: B 300 TYR cc_start: 0.2381 (OUTLIER) cc_final: 0.2074 (m-10) REVERT: B 512 MET cc_start: 0.5528 (ppp) cc_final: 0.4136 (ppp) outliers start: 37 outliers final: 20 residues processed: 64 average time/residue: 0.1648 time to fit residues: 16.0928 Evaluate side-chains 51 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 28 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8021 Z= 0.206 Angle : 0.598 9.630 10795 Z= 0.314 Chirality : 0.042 0.156 1175 Planarity : 0.004 0.054 1374 Dihedral : 9.978 85.926 1110 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.06 % Allowed : 19.61 % Favored : 76.33 % 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: -1.84 (0.26), residues: 947 helix: -0.73 (0.28), residues: 317 sheet: -1.50 (0.40), residues: 162 loop : -1.38 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 311 HIS 0.005 0.001 HIS B 205 PHE 0.011 0.001 PHE B 303 TYR 0.014 0.002 TYR A 372 ARG 0.006 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 30 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8334 (mmm) cc_final: 0.8093 (mmm) REVERT: A 156 MET cc_start: 0.8914 (ppp) cc_final: 0.8696 (ppp) REVERT: B 93 MET cc_start: 0.5712 (mmt) cc_final: 0.5165 (mmt) REVERT: B 125 MET cc_start: 0.6813 (pmm) cc_final: 0.6572 (pmm) REVERT: B 167 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8884 (m) REVERT: B 300 TYR cc_start: 0.2279 (OUTLIER) cc_final: 0.1995 (m-10) REVERT: B 512 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.4282 (ppp) outliers start: 35 outliers final: 21 residues processed: 62 average time/residue: 0.2113 time to fit residues: 18.4069 Evaluate side-chains 53 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 29 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 51 optimal weight: 0.0370 chunk 91 optimal weight: 0.0010 chunk 57 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 overall best weight: 2.5868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8021 Z= 0.188 Angle : 0.579 8.800 10795 Z= 0.304 Chirality : 0.041 0.149 1175 Planarity : 0.004 0.044 1374 Dihedral : 9.861 87.157 1110 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.48 % Allowed : 19.84 % Favored : 76.68 % 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: -1.73 (0.27), residues: 947 helix: -0.56 (0.29), residues: 315 sheet: -1.51 (0.40), residues: 162 loop : -1.35 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 311 HIS 0.004 0.001 HIS B 205 PHE 0.009 0.001 PHE B 303 TYR 0.015 0.002 TYR A 372 ARG 0.005 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 30 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.8229 (mmm) cc_final: 0.8020 (mmm) REVERT: A 156 MET cc_start: 0.8858 (ppp) cc_final: 0.8532 (ppp) REVERT: B 93 MET cc_start: 0.5779 (mmt) cc_final: 0.5037 (mmt) REVERT: B 125 MET cc_start: 0.6918 (pmm) cc_final: 0.6691 (pmm) REVERT: B 128 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: B 300 TYR cc_start: 0.2204 (OUTLIER) cc_final: 0.1994 (m-10) REVERT: B 421 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8064 (p0) REVERT: B 475 MET cc_start: 0.4213 (mtt) cc_final: 0.3846 (ptp) REVERT: B 512 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.4334 (ppp) outliers start: 30 outliers final: 19 residues processed: 59 average time/residue: 0.1769 time to fit residues: 15.6693 Evaluate side-chains 52 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 29 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 8.9990 chunk 27 optimal weight: 40.0000 chunk 17 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN B 128 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8021 Z= 0.285 Angle : 0.655 9.637 10795 Z= 0.342 Chirality : 0.042 0.149 1175 Planarity : 0.005 0.075 1374 Dihedral : 10.202 89.905 1110 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 31.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.29 % Allowed : 19.61 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.26), residues: 947 helix: -0.76 (0.28), residues: 317 sheet: -1.59 (0.40), residues: 164 loop : -1.38 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 311 HIS 0.006 0.002 HIS B 184 PHE 0.016 0.001 PHE B 129 TYR 0.031 0.002 TYR A 275 ARG 0.015 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 28 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8850 (ppp) cc_final: 0.8517 (ppp) REVERT: B 93 MET cc_start: 0.5891 (mmt) cc_final: 0.5207 (mmt) REVERT: B 125 MET cc_start: 0.6856 (pmm) cc_final: 0.6617 (pmm) REVERT: B 128 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: B 300 TYR cc_start: 0.2605 (OUTLIER) cc_final: 0.2345 (m-10) REVERT: B 421 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8079 (p0) REVERT: B 512 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.4529 (ppp) outliers start: 37 outliers final: 27 residues processed: 62 average time/residue: 0.1747 time to fit residues: 16.2981 Evaluate side-chains 59 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 28 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8021 Z= 0.243 Angle : 0.635 10.188 10795 Z= 0.331 Chirality : 0.042 0.155 1175 Planarity : 0.004 0.054 1374 Dihedral : 10.022 89.240 1110 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 29.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.94 % Allowed : 19.84 % Favored : 76.22 % 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: -1.88 (0.26), residues: 947 helix: -0.80 (0.28), residues: 317 sheet: -1.63 (0.40), residues: 156 loop : -1.35 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 311 HIS 0.006 0.002 HIS B 205 PHE 0.010 0.001 PHE B 303 TYR 0.026 0.002 TYR A 275 ARG 0.011 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 30 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8840 (ppp) cc_final: 0.8620 (ppp) REVERT: B 93 MET cc_start: 0.5969 (mmt) cc_final: 0.5290 (mmt) REVERT: B 125 MET cc_start: 0.6895 (pmm) cc_final: 0.6626 (pmm) REVERT: B 300 TYR cc_start: 0.2505 (OUTLIER) cc_final: 0.2214 (m-10) REVERT: B 421 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8146 (p0) REVERT: B 429 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7084 (t80) REVERT: B 475 MET cc_start: 0.4395 (OUTLIER) cc_final: 0.4001 (ptp) REVERT: B 512 MET cc_start: 0.5696 (OUTLIER) cc_final: 0.4585 (ppp) outliers start: 34 outliers final: 24 residues processed: 61 average time/residue: 0.1892 time to fit residues: 16.9836 Evaluate side-chains 58 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 29 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0060 chunk 62 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8021 Z= 0.165 Angle : 0.586 10.874 10795 Z= 0.305 Chirality : 0.042 0.167 1175 Planarity : 0.004 0.039 1374 Dihedral : 9.708 89.832 1110 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.02 % Allowed : 21.00 % Favored : 75.99 % 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: -1.67 (0.27), residues: 947 helix: -0.58 (0.29), residues: 315 sheet: -1.46 (0.41), residues: 154 loop : -1.27 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 311 HIS 0.006 0.001 HIS B 205 PHE 0.010 0.001 PHE B 303 TYR 0.025 0.001 TYR A 275 ARG 0.005 0.000 ARG A 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 29 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.6129 (mmt) cc_final: 0.5336 (mmt) REVERT: B 125 MET cc_start: 0.6931 (pmm) cc_final: 0.6669 (pmm) REVERT: B 300 TYR cc_start: 0.2210 (OUTLIER) cc_final: 0.1966 (m-10) REVERT: B 475 MET cc_start: 0.4108 (mtt) cc_final: 0.3793 (mpp) outliers start: 26 outliers final: 22 residues processed: 54 average time/residue: 0.1920 time to fit residues: 15.4103 Evaluate side-chains 51 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 28 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.042432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.034833 restraints weight = 94837.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.035585 restraints weight = 68516.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.036118 restraints weight = 54280.076| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8021 Z= 0.157 Angle : 0.581 10.501 10795 Z= 0.300 Chirality : 0.041 0.160 1175 Planarity : 0.004 0.036 1374 Dihedral : 9.575 89.898 1110 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.78 % Allowed : 21.58 % Favored : 75.64 % 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: -1.59 (0.27), residues: 947 helix: -0.47 (0.29), residues: 316 sheet: -1.47 (0.40), residues: 164 loop : -1.23 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 311 HIS 0.005 0.001 HIS B 205 PHE 0.009 0.001 PHE B 303 TYR 0.024 0.001 TYR A 275 ARG 0.004 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.36 seconds wall clock time: 31 minutes 31.74 seconds (1891.74 seconds total)