Starting phenix.real_space_refine on Tue Sep 24 19:01:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/09_2024/7r8d_24316.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/09_2024/7r8d_24316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/09_2024/7r8d_24316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/09_2024/7r8d_24316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/09_2024/7r8d_24316.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/09_2024/7r8d_24316.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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 68 5.16 5 C 5756 2.51 5 N 1414 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 8762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4269 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 2 Chain: "B" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4269 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.15, per 1000 atoms: 0.59 Number of scatterers: 8762 At special positions: 0 Unit cell: (102.459, 72.471, 120.785, 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 68 16.00 O 1524 8.00 N 1414 7.00 C 5756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.03 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: 2.19 Conformation dependent library (CDL) restraints added in 905.6 milliseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 60.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 173 through 186 Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.639A pdb=" N TYR A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.512A pdb=" N GLN A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 438 through 478 Proline residue: A 460 - end of helix Proline residue: A 466 - end of helix removed outlier: 3.764A pdb=" N ASN A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 510 removed outlier: 3.907A pdb=" N TYR A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Proline residue: A 496 - end of helix Proline residue: A 502 - end of helix removed outlier: 4.006A pdb=" N ILE A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 546 Processing helix chain 'A' and resid 549 through 567 removed outlier: 3.582A pdb=" N ALA A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Proline residue: A 558 - end of helix Proline residue: A 563 - end of helix removed outlier: 3.655A pdb=" N LEU A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.241A pdb=" N TRP A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 602 Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 635 through 666 removed outlier: 3.731A pdb=" N ASP A 639 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 173 through 186 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 218 through 231 Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.639A pdb=" N TYR B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 388 through 405 removed outlier: 3.512A pdb=" N GLN B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 438 through 478 Proline residue: B 460 - end of helix Proline residue: B 466 - end of helix removed outlier: 3.764A pdb=" N ASN B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 510 removed outlier: 3.907A pdb=" N TYR B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Proline residue: B 496 - end of helix Proline residue: B 502 - end of helix removed outlier: 4.006A pdb=" N ILE B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 546 Processing helix chain 'B' and resid 549 through 567 removed outlier: 3.582A pdb=" N ALA B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) Proline residue: B 558 - end of helix Proline residue: B 563 - end of helix removed outlier: 3.655A pdb=" N LEU B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 4.242A pdb=" N TRP B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 602 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 635 through 666 removed outlier: 3.731A pdb=" N ASP B 639 " --> pdb=" O LYS B 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108 removed outlier: 6.996A pdb=" N LYS A 102 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER A 83 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE A 104 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 80 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 142 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 removed outlier: 6.566A pdb=" N CYS A 160 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASP A 241 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE A 162 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER A 291 " --> pdb=" O CYS A 295 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N CYS A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 108 removed outlier: 6.996A pdb=" N LYS B 102 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER B 83 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE B 104 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 80 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 142 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.567A pdb=" N CYS B 160 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASP B 241 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 162 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 297 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER B 291 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1422 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: 2.28 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2700 1.34 - 1.46: 1937 1.46 - 1.58: 4215 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 8962 Sorted by residual: bond pdb=" C ILE A 562 " pdb=" N PRO A 563 " ideal model delta sigma weight residual 1.337 1.357 -0.020 9.80e-03 1.04e+04 4.13e+00 bond pdb=" C ILE B 562 " pdb=" N PRO B 563 " ideal model delta sigma weight residual 1.337 1.356 -0.019 9.80e-03 1.04e+04 3.84e+00 bond pdb=" C3 CLR A 801 " pdb=" O1 CLR A 801 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C3 CLR B 703 " pdb=" O1 CLR B 703 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C3 CLR B 701 " pdb=" O1 CLR B 701 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 8957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11737 1.49 - 2.97: 323 2.97 - 4.46: 53 4.46 - 5.95: 33 5.95 - 7.44: 16 Bond angle restraints: 12162 Sorted by residual: angle pdb=" C GLN B 620 " pdb=" N LYS B 621 " pdb=" CA LYS B 621 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.93e+00 angle pdb=" C GLN A 620 " pdb=" N LYS A 621 " pdb=" CA LYS A 621 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 angle pdb=" N GLY A 299 " pdb=" CA GLY A 299 " pdb=" C GLY A 299 " ideal model delta sigma weight residual 110.38 114.70 -4.32 1.42e+00 4.96e-01 9.27e+00 angle pdb=" N GLY B 299 " pdb=" CA GLY B 299 " pdb=" C GLY B 299 " ideal model delta sigma weight residual 110.38 114.69 -4.31 1.42e+00 4.96e-01 9.21e+00 angle pdb=" C13 CLR B 701 " pdb=" C17 CLR B 701 " pdb=" C20 CLR B 701 " ideal model delta sigma weight residual 119.60 112.16 7.44 3.00e+00 1.11e-01 6.14e+00 ... (remaining 12157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5116 17.52 - 35.04: 452 35.04 - 52.56: 116 52.56 - 70.07: 14 70.07 - 87.59: 12 Dihedral angle restraints: 5710 sinusoidal: 2564 harmonic: 3146 Sorted by residual: dihedral pdb=" CB GLU B 628 " pdb=" CG GLU B 628 " pdb=" CD GLU B 628 " pdb=" OE1 GLU B 628 " ideal model delta sinusoidal sigma weight residual 0.00 87.59 -87.59 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 628 " pdb=" CG GLU A 628 " pdb=" CD GLU A 628 " pdb=" OE1 GLU A 628 " ideal model delta sinusoidal sigma weight residual 0.00 87.55 -87.55 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" CB LEU B 636 " pdb=" CG LEU B 636 " ideal model delta sinusoidal sigma weight residual -180.00 -120.23 -59.77 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1300 0.072 - 0.144: 94 0.144 - 0.215: 3 0.215 - 0.287: 15 0.287 - 0.359: 8 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C14 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C15 CLR A 804 " pdb=" C8 CLR A 804 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C14 CLR B 701 " pdb=" C13 CLR B 701 " pdb=" C15 CLR B 701 " pdb=" C8 CLR B 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C14 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C15 CLR B 702 " pdb=" C8 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1417 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 465 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 466 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 465 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 466 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 466 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 466 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 416 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C THR B 416 " -0.018 2.00e-02 2.50e+03 pdb=" O THR B 416 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 417 " 0.006 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 688 2.74 - 3.28: 8712 3.28 - 3.82: 14454 3.82 - 4.36: 16851 4.36 - 4.90: 30052 Nonbonded interactions: 70757 Sorted by model distance: nonbonded pdb=" O ILE A 404 " pdb=" OG1 THR A 411 " model vdw 2.202 3.040 nonbonded pdb=" O ILE B 404 " pdb=" OG1 THR B 411 " model vdw 2.202 3.040 nonbonded pdb=" OE1 GLN B 164 " pdb=" OE1 GLN B 242 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLN A 164 " pdb=" OE1 GLN A 242 " model vdw 2.225 3.040 nonbonded pdb=" O SER A 386 " pdb=" OG SER A 386 " model vdw 2.243 3.040 ... (remaining 70752 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' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.002 0.021 8962 Z= 0.139 Angle : 0.655 7.436 12162 Z= 0.339 Chirality : 0.052 0.359 1420 Planarity : 0.003 0.037 1474 Dihedral : 14.260 87.593 3688 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.93 % Allowed : 11.16 % Favored : 86.91 % 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 (0.24), residues: 1078 helix: 0.39 (0.20), residues: 620 sheet: -0.65 (0.53), residues: 78 loop : -2.83 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 480 HIS 0.001 0.000 HIS B 618 PHE 0.006 0.001 PHE A 570 TYR 0.005 0.001 TYR A 510 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 0.948 Fit side-chains REVERT: A 166 ASP cc_start: 0.7231 (m-30) cc_final: 0.6919 (m-30) REVERT: A 198 LYS cc_start: 0.8073 (tttp) cc_final: 0.7721 (ttpt) REVERT: A 618 HIS cc_start: 0.7980 (t70) cc_final: 0.7528 (t-170) REVERT: A 659 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6703 (ttm170) REVERT: B 166 ASP cc_start: 0.7197 (m-30) cc_final: 0.6914 (m-30) REVERT: B 198 LYS cc_start: 0.8046 (tttp) cc_final: 0.7744 (ttpt) REVERT: B 618 HIS cc_start: 0.7984 (t70) cc_final: 0.7497 (t-170) REVERT: B 659 ARG cc_start: 0.7027 (ttt-90) cc_final: 0.6700 (ttm170) outliers start: 18 outliers final: 14 residues processed: 204 average time/residue: 0.2084 time to fit residues: 57.8486 Evaluate side-chains 158 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 636 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 337 ASN A 392 GLN A 620 GLN B 336 GLN B 337 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 8962 Z= 0.442 Angle : 0.684 6.621 12162 Z= 0.334 Chirality : 0.046 0.156 1420 Planarity : 0.004 0.048 1474 Dihedral : 7.423 59.269 1728 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.90 % Allowed : 12.12 % Favored : 81.97 % 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: -0.49 (0.26), residues: 1078 helix: 0.76 (0.21), residues: 650 sheet: -0.57 (0.52), residues: 78 loop : -2.35 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 511 HIS 0.005 0.001 HIS B 183 PHE 0.019 0.002 PHE B 570 TYR 0.014 0.002 TYR B 602 ARG 0.005 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 125 time to evaluate : 0.940 Fit side-chains REVERT: A 166 ASP cc_start: 0.7396 (m-30) cc_final: 0.7027 (m-30) REVERT: A 198 LYS cc_start: 0.8161 (tttp) cc_final: 0.7690 (ttpt) REVERT: A 591 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7384 (ttt-90) REVERT: A 618 HIS cc_start: 0.7974 (t70) cc_final: 0.7748 (t-170) REVERT: A 659 ARG cc_start: 0.7131 (ttt-90) cc_final: 0.6782 (ttm170) REVERT: B 166 ASP cc_start: 0.7393 (m-30) cc_final: 0.7011 (m-30) REVERT: B 198 LYS cc_start: 0.8176 (tttp) cc_final: 0.7736 (ttpt) REVERT: B 584 MET cc_start: 0.7638 (mtt) cc_final: 0.7401 (mtt) REVERT: B 591 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7382 (ttt-90) REVERT: B 618 HIS cc_start: 0.8015 (t70) cc_final: 0.7757 (t-170) REVERT: B 659 ARG cc_start: 0.7146 (ttt-90) cc_final: 0.6811 (ttm170) outliers start: 55 outliers final: 38 residues processed: 161 average time/residue: 0.1891 time to fit residues: 43.1996 Evaluate side-chains 157 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 117 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8962 Z= 0.174 Angle : 0.524 5.770 12162 Z= 0.259 Chirality : 0.039 0.140 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.937 58.622 1724 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.97 % Allowed : 14.81 % Favored : 81.22 % 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: 0.22 (0.27), residues: 1078 helix: 1.36 (0.22), residues: 644 sheet: -0.29 (0.53), residues: 78 loop : -2.07 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.002 0.000 HIS B 171 PHE 0.011 0.001 PHE A 570 TYR 0.007 0.001 TYR A 602 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 0.942 Fit side-chains REVERT: A 166 ASP cc_start: 0.7333 (m-30) cc_final: 0.6981 (m-30) REVERT: A 198 LYS cc_start: 0.8197 (tttp) cc_final: 0.7722 (ttpt) REVERT: A 568 SER cc_start: 0.8627 (t) cc_final: 0.8399 (t) REVERT: A 591 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7405 (tmt-80) REVERT: A 659 ARG cc_start: 0.7109 (ttt-90) cc_final: 0.6808 (ttm170) REVERT: B 166 ASP cc_start: 0.7321 (m-30) cc_final: 0.6957 (m-30) REVERT: B 198 LYS cc_start: 0.8186 (tttp) cc_final: 0.7754 (ttpt) REVERT: B 568 SER cc_start: 0.8635 (t) cc_final: 0.8398 (t) REVERT: B 584 MET cc_start: 0.7595 (mtt) cc_final: 0.7345 (mtt) REVERT: B 591 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7390 (tmt-80) REVERT: B 659 ARG cc_start: 0.7120 (ttt-90) cc_final: 0.6801 (ttm170) outliers start: 37 outliers final: 27 residues processed: 154 average time/residue: 0.1896 time to fit residues: 41.5160 Evaluate side-chains 147 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8962 Z= 0.204 Angle : 0.534 5.933 12162 Z= 0.262 Chirality : 0.040 0.138 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.505 58.034 1718 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.83 % Allowed : 15.56 % Favored : 79.61 % 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: 0.42 (0.27), residues: 1078 helix: 1.47 (0.22), residues: 648 sheet: -0.11 (0.55), residues: 78 loop : -1.97 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 583 HIS 0.002 0.001 HIS B 171 PHE 0.013 0.001 PHE A 570 TYR 0.008 0.001 TYR B 592 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 123 time to evaluate : 0.866 Fit side-chains REVERT: A 82 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7797 (tt) REVERT: A 166 ASP cc_start: 0.7347 (m-30) cc_final: 0.6994 (m-30) REVERT: A 198 LYS cc_start: 0.8207 (tttp) cc_final: 0.7730 (ttpt) REVERT: A 568 SER cc_start: 0.8775 (t) cc_final: 0.8546 (t) REVERT: A 591 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7448 (tmt-80) REVERT: A 659 ARG cc_start: 0.7124 (ttt-90) cc_final: 0.6812 (ttm170) REVERT: B 82 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7829 (tt) REVERT: B 166 ASP cc_start: 0.7339 (m-30) cc_final: 0.6971 (m-30) REVERT: B 198 LYS cc_start: 0.8186 (tttp) cc_final: 0.7733 (ttpt) REVERT: B 568 SER cc_start: 0.8766 (t) cc_final: 0.8543 (t) REVERT: B 584 MET cc_start: 0.7590 (mtt) cc_final: 0.7365 (mtt) REVERT: B 591 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7456 (tmt-80) REVERT: B 659 ARG cc_start: 0.7111 (ttt-90) cc_final: 0.6793 (ttm170) outliers start: 45 outliers final: 33 residues processed: 153 average time/residue: 0.1841 time to fit residues: 40.0069 Evaluate side-chains 151 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.0470 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8962 Z= 0.147 Angle : 0.498 6.415 12162 Z= 0.246 Chirality : 0.038 0.138 1420 Planarity : 0.003 0.044 1474 Dihedral : 6.348 59.460 1718 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.04 % Allowed : 16.52 % Favored : 78.43 % 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: 0.73 (0.27), residues: 1078 helix: 1.69 (0.22), residues: 648 sheet: 0.11 (0.55), residues: 78 loop : -1.79 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.002 0.000 HIS B 171 PHE 0.009 0.001 PHE A 570 TYR 0.007 0.001 TYR A 510 ARG 0.002 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 127 time to evaluate : 1.034 Fit side-chains REVERT: A 166 ASP cc_start: 0.7267 (m-30) cc_final: 0.6891 (m-30) REVERT: A 198 LYS cc_start: 0.8191 (tttp) cc_final: 0.7709 (ttpt) REVERT: A 568 SER cc_start: 0.8671 (t) cc_final: 0.8413 (t) REVERT: A 591 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7602 (tmt-80) REVERT: A 659 ARG cc_start: 0.7099 (ttt-90) cc_final: 0.6795 (ttm170) REVERT: B 166 ASP cc_start: 0.7268 (m-30) cc_final: 0.6893 (m-30) REVERT: B 198 LYS cc_start: 0.8158 (tttp) cc_final: 0.7711 (ttpt) REVERT: B 568 SER cc_start: 0.8654 (t) cc_final: 0.8408 (t) REVERT: B 584 MET cc_start: 0.7524 (mtt) cc_final: 0.7312 (mtt) REVERT: B 591 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7601 (tmt-80) REVERT: B 659 ARG cc_start: 0.7107 (ttt-90) cc_final: 0.6794 (ttm170) outliers start: 47 outliers final: 36 residues processed: 156 average time/residue: 0.1846 time to fit residues: 41.3608 Evaluate side-chains 159 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8962 Z= 0.387 Angle : 0.641 6.678 12162 Z= 0.312 Chirality : 0.045 0.148 1420 Planarity : 0.004 0.046 1474 Dihedral : 6.652 56.621 1717 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.22 % Allowed : 15.67 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.27), residues: 1078 helix: 1.27 (0.21), residues: 654 sheet: -0.06 (0.54), residues: 78 loop : -1.88 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 480 HIS 0.003 0.001 HIS A 183 PHE 0.016 0.002 PHE A 570 TYR 0.014 0.002 TYR A 592 ARG 0.003 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 121 time to evaluate : 0.844 Fit side-chains REVERT: A 82 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7768 (tt) REVERT: A 166 ASP cc_start: 0.7370 (m-30) cc_final: 0.6974 (m-30) REVERT: A 198 LYS cc_start: 0.8158 (tttp) cc_final: 0.7680 (ttpt) REVERT: A 319 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8509 (m-70) REVERT: A 591 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7505 (ttt-90) REVERT: A 659 ARG cc_start: 0.7200 (ttt-90) cc_final: 0.6878 (ttm170) REVERT: B 82 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 166 ASP cc_start: 0.7373 (m-30) cc_final: 0.6980 (m-30) REVERT: B 198 LYS cc_start: 0.8140 (tttp) cc_final: 0.7671 (ttpt) REVERT: B 591 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7503 (ttt-90) REVERT: B 659 ARG cc_start: 0.7214 (ttt-90) cc_final: 0.6889 (ttm170) outliers start: 58 outliers final: 42 residues processed: 160 average time/residue: 0.1830 time to fit residues: 42.7581 Evaluate side-chains 160 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 113 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8962 Z= 0.186 Angle : 0.530 7.458 12162 Z= 0.261 Chirality : 0.039 0.138 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.292 55.650 1717 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.94 % Allowed : 17.38 % Favored : 77.68 % 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: 0.64 (0.27), residues: 1078 helix: 1.58 (0.21), residues: 652 sheet: 0.07 (0.55), residues: 78 loop : -1.77 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 583 HIS 0.003 0.001 HIS B 171 PHE 0.010 0.001 PHE A 465 TYR 0.008 0.001 TYR B 510 ARG 0.002 0.000 ARG B 651 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 123 time to evaluate : 0.836 Fit side-chains REVERT: A 166 ASP cc_start: 0.7296 (m-30) cc_final: 0.6908 (m-30) REVERT: A 198 LYS cc_start: 0.8141 (tttp) cc_final: 0.7668 (ttpt) REVERT: A 319 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.8493 (m-70) REVERT: A 591 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7607 (tmt-80) REVERT: A 628 GLU cc_start: 0.7775 (tp30) cc_final: 0.7482 (tp30) REVERT: A 659 ARG cc_start: 0.7146 (ttt-90) cc_final: 0.6818 (ttm170) REVERT: B 166 ASP cc_start: 0.7298 (m-30) cc_final: 0.6908 (m-30) REVERT: B 198 LYS cc_start: 0.8177 (tttp) cc_final: 0.7713 (ttpt) REVERT: B 591 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7606 (tmt-80) REVERT: B 628 GLU cc_start: 0.7755 (tp30) cc_final: 0.7471 (tp30) REVERT: B 659 ARG cc_start: 0.7147 (ttt-90) cc_final: 0.6828 (ttm170) outliers start: 46 outliers final: 37 residues processed: 153 average time/residue: 0.1764 time to fit residues: 38.7402 Evaluate side-chains 160 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8962 Z= 0.219 Angle : 0.555 7.750 12162 Z= 0.269 Chirality : 0.040 0.139 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.276 54.328 1717 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.72 % Allowed : 17.49 % Favored : 77.79 % 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: 0.76 (0.27), residues: 1078 helix: 1.67 (0.21), residues: 648 sheet: 0.17 (0.55), residues: 78 loop : -1.70 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 583 HIS 0.005 0.001 HIS B 618 PHE 0.011 0.001 PHE A 570 TYR 0.007 0.001 TYR B 602 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 124 time to evaluate : 0.927 Fit side-chains REVERT: A 166 ASP cc_start: 0.7301 (m-30) cc_final: 0.6917 (m-30) REVERT: A 198 LYS cc_start: 0.8135 (tttp) cc_final: 0.7664 (ttpt) REVERT: A 319 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.8483 (m-70) REVERT: A 591 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7614 (tmt-80) REVERT: A 628 GLU cc_start: 0.7799 (tp30) cc_final: 0.7498 (tp30) REVERT: A 659 ARG cc_start: 0.7158 (ttt-90) cc_final: 0.6833 (ttm170) REVERT: B 166 ASP cc_start: 0.7304 (m-30) cc_final: 0.6919 (m-30) REVERT: B 198 LYS cc_start: 0.8138 (tttp) cc_final: 0.7660 (ttpt) REVERT: B 591 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7614 (tmt-80) REVERT: B 628 GLU cc_start: 0.7787 (tp30) cc_final: 0.7496 (tp30) REVERT: B 659 ARG cc_start: 0.7158 (ttt-90) cc_final: 0.6835 (ttm170) outliers start: 44 outliers final: 37 residues processed: 154 average time/residue: 0.1794 time to fit residues: 39.8984 Evaluate side-chains 163 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8962 Z= 0.162 Angle : 0.526 8.329 12162 Z= 0.256 Chirality : 0.039 0.138 1420 Planarity : 0.003 0.045 1474 Dihedral : 6.044 53.734 1715 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.08 % Allowed : 17.92 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1078 helix: 1.84 (0.22), residues: 648 sheet: 0.32 (0.56), residues: 78 loop : -1.58 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 583 HIS 0.003 0.001 HIS B 171 PHE 0.010 0.001 PHE A 570 TYR 0.006 0.001 TYR B 429 ARG 0.001 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 1.042 Fit side-chains REVERT: A 166 ASP cc_start: 0.7242 (m-30) cc_final: 0.6852 (m-30) REVERT: A 198 LYS cc_start: 0.8138 (tttp) cc_final: 0.7660 (ttpt) REVERT: A 319 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8490 (m-70) REVERT: A 591 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7621 (tmt-80) REVERT: A 628 GLU cc_start: 0.7749 (tp30) cc_final: 0.7444 (tp30) REVERT: A 659 ARG cc_start: 0.7133 (ttt-90) cc_final: 0.6816 (ttm170) REVERT: B 166 ASP cc_start: 0.7247 (m-30) cc_final: 0.6858 (m-30) REVERT: B 198 LYS cc_start: 0.8185 (tttp) cc_final: 0.7711 (ttpt) REVERT: B 591 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7617 (tmt-80) REVERT: B 628 GLU cc_start: 0.7737 (tp30) cc_final: 0.7441 (tp30) REVERT: B 659 ARG cc_start: 0.7131 (ttt-90) cc_final: 0.6816 (ttm170) outliers start: 38 outliers final: 34 residues processed: 153 average time/residue: 0.1872 time to fit residues: 41.5751 Evaluate side-chains 161 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 8962 Z= 0.432 Angle : 0.666 8.104 12162 Z= 0.322 Chirality : 0.046 0.150 1420 Planarity : 0.004 0.046 1474 Dihedral : 6.453 49.592 1715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.51 % Allowed : 17.38 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1078 helix: 1.40 (0.21), residues: 650 sheet: 0.01 (0.54), residues: 78 loop : -1.77 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 480 HIS 0.004 0.001 HIS A 618 PHE 0.016 0.002 PHE A 465 TYR 0.012 0.002 TYR A 592 ARG 0.003 0.000 ARG A 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 0.962 Fit side-chains REVERT: A 166 ASP cc_start: 0.7327 (m-30) cc_final: 0.6929 (m-30) REVERT: A 198 LYS cc_start: 0.8155 (tttp) cc_final: 0.7721 (ttpt) REVERT: A 319 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8496 (m-70) REVERT: A 440 LEU cc_start: 0.7940 (mt) cc_final: 0.7724 (mt) REVERT: A 591 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7610 (ttt-90) REVERT: A 628 GLU cc_start: 0.7923 (tp30) cc_final: 0.7642 (tp30) REVERT: A 659 ARG cc_start: 0.7227 (ttt-90) cc_final: 0.6888 (ttm170) REVERT: B 166 ASP cc_start: 0.7331 (m-30) cc_final: 0.6931 (m-30) REVERT: B 198 LYS cc_start: 0.8167 (tttp) cc_final: 0.7737 (ttpt) REVERT: B 591 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7609 (ttt-90) REVERT: B 628 GLU cc_start: 0.7909 (tp30) cc_final: 0.7504 (tp30) REVERT: B 659 ARG cc_start: 0.7219 (ttt-90) cc_final: 0.6844 (ttm170) outliers start: 42 outliers final: 36 residues processed: 143 average time/residue: 0.1868 time to fit residues: 38.6753 Evaluate side-chains 153 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** 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 = 0.3242 r_free = 0.3242 target = 0.116612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.091215 restraints weight = 10153.579| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.96 r_work: 0.3000 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8962 Z= 0.239 Angle : 0.577 8.392 12162 Z= 0.280 Chirality : 0.041 0.138 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.193 49.381 1715 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.18 % Allowed : 17.70 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 1078 helix: 1.57 (0.21), residues: 652 sheet: 0.05 (0.54), residues: 78 loop : -1.67 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 583 HIS 0.004 0.001 HIS A 618 PHE 0.012 0.001 PHE A 570 TYR 0.008 0.001 TYR A 429 ARG 0.002 0.000 ARG A 156 =============================================================================== Job complete usr+sys time: 1906.79 seconds wall clock time: 39 minutes 52.57 seconds (2392.57 seconds total)