Starting phenix.real_space_refine on Wed Sep 25 04:56:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/09_2024/7xf5_33169.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/09_2024/7xf5_33169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/09_2024/7xf5_33169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/09_2024/7xf5_33169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/09_2024/7xf5_33169.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/09_2024/7xf5_33169.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6294 2.51 5 N 1615 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4837 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 29, 'TRANS': 592} Chain breaks: 3 Chain: "B" Number of atoms: 4803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4803 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 28, 'TRANS': 588} Chain breaks: 3 Time building chain proxies: 5.89, per 1000 atoms: 0.61 Number of scatterers: 9640 At special positions: 0 Unit cell: (111.915, 113.573, 116.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1674 8.00 N 1615 7.00 C 6294 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 3 sheets defined 74.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 129 through 156 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 181 through 198 Processing helix chain 'A' and resid 204 through 225 Processing helix chain 'A' and resid 226 through 231 removed outlier: 6.910A pdb=" N ILE A 229 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.609A pdb=" N PHE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.614A pdb=" N SER A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.514A pdb=" N GLN A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 364 through 378 removed outlier: 3.556A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.726A pdb=" N GLN A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 430 through 450 removed outlier: 4.142A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.872A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.425A pdb=" N VAL A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 549 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.828A pdb=" N TYR A 576 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 578 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 596 through 607 removed outlier: 4.203A pdb=" N LEU A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 640 removed outlier: 3.643A pdb=" N LEU A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.706A pdb=" N ARG A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 778 removed outlier: 4.057A pdb=" N ILE A 771 " --> pdb=" O SER A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 814 removed outlier: 3.709A pdb=" N LEU A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 844 removed outlier: 4.120A pdb=" N LEU A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 126 removed outlier: 3.514A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.854A pdb=" N LEU B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 7.085A pdb=" N ILE B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.647A pdb=" N PHE B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.716A pdb=" N VAL B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 296 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.574A pdb=" N ALA B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.674A pdb=" N GLN B 385 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 430 through 450 removed outlier: 4.073A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.866A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 530 through 549 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.847A pdb=" N TYR B 576 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 578 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.576A pdb=" N MET B 584 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 removed outlier: 3.867A pdb=" N LEU B 600 " --> pdb=" O THR B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 640 removed outlier: 3.751A pdb=" N LEU B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 648 removed outlier: 4.552A pdb=" N ARG B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 648 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 778 Processing helix chain 'B' and resid 802 through 810 Processing helix chain 'B' and resid 832 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487 649 hydrogen bonds defined for protein. 1860 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: 2.63 Time building geometry restraints manager: 2.95 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: 3038 1.34 - 1.46: 2194 1.46 - 1.58: 4533 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9861 Sorted by residual: bond pdb=" CA LEU B 812 " pdb=" C LEU B 812 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.34e-02 5.57e+03 4.52e+00 bond pdb=" CA LEU B 813 " pdb=" C LEU B 813 " ideal model delta sigma weight residual 1.521 1.503 0.018 1.36e-02 5.41e+03 1.71e+00 bond pdb=" N ILE B 170 " pdb=" CA ILE B 170 " ideal model delta sigma weight residual 1.461 1.447 0.014 1.19e-02 7.06e+03 1.34e+00 bond pdb=" C LYS B 168 " pdb=" O LYS B 168 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.19e-02 7.06e+03 1.30e+00 bond pdb=" C THR B 169 " pdb=" O THR B 169 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.19e-02 7.06e+03 1.30e+00 ... (remaining 9856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 13301 2.71 - 5.43: 86 5.43 - 8.14: 8 8.14 - 10.86: 3 10.86 - 13.57: 1 Bond angle restraints: 13399 Sorted by residual: angle pdb=" N LEU B 813 " pdb=" CA LEU B 813 " pdb=" C LEU B 813 " ideal model delta sigma weight residual 113.41 99.84 13.57 1.22e+00 6.72e-01 1.24e+02 angle pdb=" N SER B 811 " pdb=" CA SER B 811 " pdb=" C SER B 811 " ideal model delta sigma weight residual 114.64 109.05 5.59 1.52e+00 4.33e-01 1.35e+01 angle pdb=" N PHE B 810 " pdb=" CA PHE B 810 " pdb=" C PHE B 810 " ideal model delta sigma weight residual 113.37 108.50 4.87 1.38e+00 5.25e-01 1.25e+01 angle pdb=" CB MET A 167 " pdb=" CG MET A 167 " pdb=" SD MET A 167 " ideal model delta sigma weight residual 112.70 104.08 8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" C TYR B 230 " pdb=" N GLU B 231 " pdb=" CA GLU B 231 " ideal model delta sigma weight residual 121.94 116.23 5.71 2.00e+00 2.50e-01 8.16e+00 ... (remaining 13394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5322 17.22 - 34.43: 377 34.43 - 51.65: 81 51.65 - 68.87: 27 68.87 - 86.08: 22 Dihedral angle restraints: 5829 sinusoidal: 2262 harmonic: 3567 Sorted by residual: dihedral pdb=" CB GLU B 166 " pdb=" CG GLU B 166 " pdb=" CD GLU B 166 " pdb=" OE1 GLU B 166 " ideal model delta sinusoidal sigma weight residual 0.00 -85.33 85.33 1 3.00e+01 1.11e-03 9.80e+00 dihedral pdb=" CA LEU B 813 " pdb=" CB LEU B 813 " pdb=" CG LEU B 813 " pdb=" CD1 LEU B 813 " ideal model delta sinusoidal sigma weight residual 60.00 116.27 -56.27 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CG ARG A 558 " pdb=" CD ARG A 558 " pdb=" NE ARG A 558 " pdb=" CZ ARG A 558 " ideal model delta sinusoidal sigma weight residual -180.00 -138.50 -41.50 2 1.50e+01 4.44e-03 9.37e+00 ... (remaining 5826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1194 0.043 - 0.085: 298 0.085 - 0.127: 79 0.127 - 0.170: 5 0.170 - 0.212: 2 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA LEU B 813 " pdb=" N LEU B 813 " pdb=" C LEU B 813 " pdb=" CB LEU B 813 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LEU B 812 " pdb=" N LEU B 812 " pdb=" C LEU B 812 " pdb=" CB LEU B 812 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA GLU B 231 " pdb=" N GLU B 231 " pdb=" C GLU B 231 " pdb=" CB GLU B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1575 not shown) Planarity restraints: 1671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 444 " -0.019 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP A 444 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 444 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 444 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 444 " 0.012 2.00e-02 2.50e+03 1.25e-02 3.89e+00 pdb=" CG TRP B 444 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 444 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 444 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 444 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 379 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 380 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.022 5.00e-02 4.00e+02 ... (remaining 1668 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1459 2.76 - 3.29: 9581 3.29 - 3.83: 16013 3.83 - 4.36: 17154 4.36 - 4.90: 30157 Nonbonded interactions: 74364 Sorted by model distance: nonbonded pdb=" OE2 GLU A 320 " pdb=" OH TYR A 499 " model vdw 2.222 3.040 nonbonded pdb=" OE2 GLU B 320 " pdb=" OH TYR B 499 " model vdw 2.226 3.040 nonbonded pdb=" O GLU A 166 " pdb=" OG1 THR A 169 " model vdw 2.233 3.040 nonbonded pdb=" O ASP A 402 " pdb=" NH1 ARG A 471 " model vdw 2.284 3.120 nonbonded pdb=" O ARG B 601 " pdb=" ND1 HIS B 605 " model vdw 2.308 3.120 ... (remaining 74359 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 89 through 649 or resid 769 through 845)) selection = chain 'B' } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.580 Find NCS groups from input model: 0.330 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 : 0.003 0.045 9861 Z= 0.164 Angle : 0.607 13.571 13399 Z= 0.348 Chirality : 0.040 0.212 1578 Planarity : 0.004 0.040 1671 Dihedral : 14.141 86.085 3517 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 0.58 % Allowed : 0.29 % Favored : 99.13 % 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: 1.11 (0.24), residues: 1223 helix: 1.51 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.93 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 444 HIS 0.012 0.001 HIS B 210 PHE 0.021 0.001 PHE B 147 TYR 0.016 0.001 TYR A 140 ARG 0.011 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 344 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 HIS cc_start: 0.7891 (t-170) cc_final: 0.7565 (t70) REVERT: A 239 MET cc_start: 0.7214 (mmt) cc_final: 0.6759 (ptm) REVERT: A 309 ARG cc_start: 0.6994 (ttp-170) cc_final: 0.6200 (mtm110) REVERT: A 340 TYR cc_start: 0.6818 (t80) cc_final: 0.6472 (t80) REVERT: A 374 ILE cc_start: 0.8639 (tt) cc_final: 0.8155 (mt) REVERT: A 439 ILE cc_start: 0.8192 (mm) cc_final: 0.7980 (mt) REVERT: A 531 ILE cc_start: 0.9316 (tt) cc_final: 0.9045 (tt) REVERT: A 549 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7359 (tt0) REVERT: A 558 ARG cc_start: 0.6490 (mmt180) cc_final: 0.5991 (mtt-85) REVERT: A 801 THR cc_start: 0.5389 (m) cc_final: 0.5177 (m) REVERT: B 219 LEU cc_start: 0.8581 (tp) cc_final: 0.8373 (tp) REVERT: B 374 ILE cc_start: 0.8657 (tt) cc_final: 0.8180 (mt) REVERT: B 558 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5626 (mtt180) REVERT: B 815 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.5240 (m) outliers start: 6 outliers final: 1 residues processed: 347 average time/residue: 0.2238 time to fit residues: 105.5225 Evaluate side-chains 217 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 133 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS A 530 HIS A 546 GLN B 133 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9861 Z= 0.364 Angle : 0.710 9.040 13399 Z= 0.367 Chirality : 0.048 0.227 1578 Planarity : 0.005 0.043 1671 Dihedral : 4.467 50.717 1324 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.01 % Allowed : 9.51 % Favored : 87.48 % 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: 0.86 (0.24), residues: 1223 helix: 1.29 (0.17), residues: 827 sheet: None (None), residues: 0 loop : -0.92 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 91 HIS 0.007 0.001 HIS B 210 PHE 0.027 0.003 PHE B 522 TYR 0.025 0.003 TYR B 134 ARG 0.005 0.001 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.7373 (ttp-170) cc_final: 0.7075 (mtm110) REVERT: A 374 ILE cc_start: 0.8578 (tt) cc_final: 0.8137 (mt) REVERT: A 453 PRO cc_start: 0.8357 (Cg_endo) cc_final: 0.8133 (Cg_exo) REVERT: A 540 LEU cc_start: 0.9231 (mt) cc_final: 0.9026 (mp) REVERT: B 178 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6051 (pm20) REVERT: B 214 MET cc_start: 0.7728 (mtp) cc_final: 0.7471 (mtp) REVERT: B 252 PHE cc_start: 0.5851 (m-80) cc_final: 0.5003 (m-80) REVERT: B 374 ILE cc_start: 0.8634 (tt) cc_final: 0.8363 (mt) REVERT: B 383 PHE cc_start: 0.8360 (t80) cc_final: 0.8039 (t80) REVERT: B 453 PRO cc_start: 0.8412 (Cg_endo) cc_final: 0.8172 (Cg_exo) outliers start: 31 outliers final: 20 residues processed: 269 average time/residue: 0.2039 time to fit residues: 76.9202 Evaluate side-chains 234 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 213 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN A 409 GLN B 133 GLN B 422 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9861 Z= 0.179 Angle : 0.569 13.770 13399 Z= 0.286 Chirality : 0.042 0.153 1578 Planarity : 0.004 0.035 1671 Dihedral : 3.680 18.642 1321 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.43 % Allowed : 13.79 % Favored : 83.79 % 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: 1.34 (0.24), residues: 1223 helix: 1.72 (0.18), residues: 827 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 91 HIS 0.005 0.001 HIS A 513 PHE 0.015 0.001 PHE B 185 TYR 0.020 0.001 TYR B 140 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7536 (mt0) cc_final: 0.7058 (tp40) REVERT: A 274 ASN cc_start: 0.8183 (m-40) cc_final: 0.7964 (m110) REVERT: A 309 ARG cc_start: 0.7400 (ttp-170) cc_final: 0.5945 (ttp-170) REVERT: A 314 PHE cc_start: 0.5773 (m-80) cc_final: 0.5502 (m-80) REVERT: A 374 ILE cc_start: 0.8557 (tt) cc_final: 0.8354 (mt) REVERT: A 477 MET cc_start: 0.7618 (mmm) cc_final: 0.7402 (mmm) REVERT: B 344 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7669 (mmmm) REVERT: B 383 PHE cc_start: 0.8305 (t80) cc_final: 0.8027 (t80) REVERT: B 453 PRO cc_start: 0.8386 (Cg_endo) cc_final: 0.8185 (Cg_exo) outliers start: 25 outliers final: 16 residues processed: 232 average time/residue: 0.2056 time to fit residues: 67.2501 Evaluate side-chains 221 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 816 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 133 GLN B 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9861 Z= 0.170 Angle : 0.562 13.968 13399 Z= 0.277 Chirality : 0.042 0.298 1578 Planarity : 0.004 0.054 1671 Dihedral : 3.533 16.847 1321 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 13.11 % Favored : 84.17 % 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: 1.47 (0.24), residues: 1223 helix: 1.81 (0.18), residues: 829 sheet: None (None), residues: 0 loop : -0.84 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 444 HIS 0.005 0.001 HIS B 210 PHE 0.017 0.001 PHE A 287 TYR 0.014 0.001 TYR A 140 ARG 0.003 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5756 (m-80) cc_final: 0.5510 (m-80) REVERT: A 477 MET cc_start: 0.7707 (mmm) cc_final: 0.7457 (mmm) REVERT: B 292 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 344 LYS cc_start: 0.7967 (mmtm) cc_final: 0.7695 (mmmm) REVERT: B 383 PHE cc_start: 0.8324 (t80) cc_final: 0.8031 (t80) REVERT: B 453 PRO cc_start: 0.8446 (Cg_endo) cc_final: 0.8204 (Cg_exo) outliers start: 28 outliers final: 19 residues processed: 234 average time/residue: 0.2239 time to fit residues: 73.8215 Evaluate side-chains 226 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.0030 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9861 Z= 0.236 Angle : 0.617 15.345 13399 Z= 0.305 Chirality : 0.043 0.170 1578 Planarity : 0.005 0.049 1671 Dihedral : 3.662 17.336 1321 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.40 % Allowed : 15.24 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1223 helix: 1.73 (0.18), residues: 829 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 276 HIS 0.004 0.001 HIS A 513 PHE 0.026 0.002 PHE A 289 TYR 0.015 0.002 TYR A 140 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 223 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 TYR cc_start: 0.7062 (t80) cc_final: 0.6850 (t80) REVERT: B 218 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6509 (mt) REVERT: B 383 PHE cc_start: 0.8261 (t80) cc_final: 0.7959 (t80) outliers start: 35 outliers final: 28 residues processed: 239 average time/residue: 0.2049 time to fit residues: 68.9325 Evaluate side-chains 242 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 chunk 55 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9861 Z= 0.195 Angle : 0.604 15.849 13399 Z= 0.293 Chirality : 0.043 0.247 1578 Planarity : 0.004 0.058 1671 Dihedral : 3.587 15.742 1321 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.40 % Allowed : 16.89 % Favored : 79.71 % 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 (0.24), residues: 1223 helix: 1.79 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 276 HIS 0.004 0.001 HIS A 513 PHE 0.018 0.001 PHE A 279 TYR 0.017 0.001 TYR A 140 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 216 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5854 (m-80) cc_final: 0.5590 (m-80) REVERT: A 340 TYR cc_start: 0.7009 (t80) cc_final: 0.6800 (t80) REVERT: B 218 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.6528 (mt) REVERT: B 276 TRP cc_start: 0.7161 (m-10) cc_final: 0.6925 (t60) REVERT: B 344 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7607 (mmmm) REVERT: B 383 PHE cc_start: 0.8278 (t80) cc_final: 0.7982 (t80) outliers start: 35 outliers final: 24 residues processed: 232 average time/residue: 0.2076 time to fit residues: 67.8829 Evaluate side-chains 234 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 50.0000 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 133 GLN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9861 Z= 0.181 Angle : 0.594 14.088 13399 Z= 0.290 Chirality : 0.043 0.173 1578 Planarity : 0.004 0.056 1671 Dihedral : 3.559 16.048 1321 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.20 % Allowed : 18.83 % 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: 1.61 (0.24), residues: 1223 helix: 1.87 (0.18), residues: 827 sheet: None (None), residues: 0 loop : -0.64 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 276 HIS 0.006 0.001 HIS A 210 PHE 0.024 0.001 PHE B 93 TYR 0.018 0.001 TYR B 140 ARG 0.008 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5834 (m-80) cc_final: 0.5449 (m-80) REVERT: A 340 TYR cc_start: 0.7044 (t80) cc_final: 0.6774 (t80) REVERT: B 218 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6578 (mt) REVERT: B 276 TRP cc_start: 0.7251 (m-10) cc_final: 0.6911 (t60) REVERT: B 344 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7633 (mmmm) REVERT: B 383 PHE cc_start: 0.8219 (t80) cc_final: 0.7885 (t80) outliers start: 33 outliers final: 27 residues processed: 235 average time/residue: 0.2050 time to fit residues: 67.7240 Evaluate side-chains 245 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9861 Z= 0.194 Angle : 0.616 14.822 13399 Z= 0.298 Chirality : 0.042 0.171 1578 Planarity : 0.004 0.059 1671 Dihedral : 3.557 17.046 1321 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.20 % Allowed : 19.32 % Favored : 77.48 % 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 (0.24), residues: 1223 helix: 1.82 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.55 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 276 HIS 0.005 0.001 HIS A 210 PHE 0.024 0.001 PHE B 287 TYR 0.021 0.001 TYR B 140 ARG 0.007 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5748 (m-80) cc_final: 0.5522 (m-80) REVERT: A 340 TYR cc_start: 0.7104 (t80) cc_final: 0.6856 (t80) REVERT: B 276 TRP cc_start: 0.7233 (m-10) cc_final: 0.6766 (t60) REVERT: B 340 TYR cc_start: 0.7278 (t80) cc_final: 0.7045 (t80) REVERT: B 344 LYS cc_start: 0.7997 (mmtm) cc_final: 0.7685 (mmmm) REVERT: B 383 PHE cc_start: 0.8223 (t80) cc_final: 0.7841 (t80) REVERT: B 611 MET cc_start: 0.1076 (mmp) cc_final: 0.0771 (mtp) REVERT: B 832 LEU cc_start: -0.2648 (OUTLIER) cc_final: -0.3004 (mp) outliers start: 33 outliers final: 24 residues processed: 232 average time/residue: 0.2008 time to fit residues: 65.7425 Evaluate side-chains 241 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 832 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 113 optimal weight: 0.0050 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.0050 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9861 Z= 0.175 Angle : 0.613 14.520 13399 Z= 0.295 Chirality : 0.042 0.197 1578 Planarity : 0.004 0.060 1671 Dihedral : 3.515 16.491 1321 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.43 % Allowed : 19.71 % Favored : 77.86 % 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: 1.60 (0.24), residues: 1223 helix: 1.81 (0.18), residues: 835 sheet: None (None), residues: 0 loop : -0.57 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.004 0.001 HIS A 210 PHE 0.026 0.001 PHE B 287 TYR 0.026 0.001 TYR B 140 ARG 0.007 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5838 (m-80) cc_final: 0.5329 (m-80) REVERT: A 340 TYR cc_start: 0.7108 (t80) cc_final: 0.6799 (t80) REVERT: B 276 TRP cc_start: 0.7182 (m-10) cc_final: 0.6865 (t60) REVERT: B 344 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7648 (mmmm) REVERT: B 383 PHE cc_start: 0.8180 (t80) cc_final: 0.7772 (t80) REVERT: B 832 LEU cc_start: -0.2702 (OUTLIER) cc_final: -0.3037 (mp) outliers start: 25 outliers final: 20 residues processed: 230 average time/residue: 0.2043 time to fit residues: 65.8886 Evaluate side-chains 233 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 832 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9861 Z= 0.202 Angle : 0.649 14.988 13399 Z= 0.312 Chirality : 0.043 0.189 1578 Planarity : 0.005 0.062 1671 Dihedral : 3.541 16.452 1321 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.23 % Allowed : 20.29 % Favored : 77.48 % 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 (0.25), residues: 1223 helix: 1.76 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.48 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 121 HIS 0.004 0.001 HIS A 817 PHE 0.035 0.001 PHE B 287 TYR 0.025 0.001 TYR B 140 ARG 0.007 0.000 ARG A 297 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 TYR cc_start: 0.7101 (t80) cc_final: 0.6824 (t80) REVERT: B 205 GLU cc_start: 0.7248 (pm20) cc_final: 0.6980 (pm20) REVERT: B 276 TRP cc_start: 0.7202 (m-10) cc_final: 0.6915 (t60) REVERT: B 340 TYR cc_start: 0.7140 (t80) cc_final: 0.6831 (t80) REVERT: B 344 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7701 (mmmm) REVERT: B 383 PHE cc_start: 0.8186 (t80) cc_final: 0.7802 (t80) REVERT: B 611 MET cc_start: 0.1260 (mmp) cc_final: 0.0877 (mtp) REVERT: B 832 LEU cc_start: -0.2684 (OUTLIER) cc_final: -0.2997 (mp) outliers start: 23 outliers final: 21 residues processed: 223 average time/residue: 0.2145 time to fit residues: 66.7283 Evaluate side-chains 231 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 209 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 832 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.196312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151067 restraints weight = 15616.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154444 restraints weight = 9063.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156817 restraints weight = 6355.063| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9861 Z= 0.187 Angle : 0.625 14.829 13399 Z= 0.302 Chirality : 0.043 0.196 1578 Planarity : 0.004 0.062 1671 Dihedral : 3.522 16.346 1321 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.43 % Allowed : 20.00 % Favored : 77.57 % 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 (0.25), residues: 1223 helix: 1.78 (0.18), residues: 837 sheet: None (None), residues: 0 loop : -0.48 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.004 0.001 HIS A 513 PHE 0.037 0.001 PHE B 287 TYR 0.026 0.001 TYR B 140 ARG 0.008 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.43 seconds wall clock time: 41 minutes 23.79 seconds (2483.79 seconds total)