Starting phenix.real_space_refine on Sat Dec 28 10:02:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uve_42617/12_2024/8uve_42617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uve_42617/12_2024/8uve_42617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uve_42617/12_2024/8uve_42617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uve_42617/12_2024/8uve_42617.map" model { file = "/net/cci-nas-00/data/ceres_data/8uve_42617/12_2024/8uve_42617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uve_42617/12_2024/8uve_42617.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 51 5.16 5 Na 2 4.78 5 C 5730 2.51 5 N 1249 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8373 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3887 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 33, 'TRANS': 463} Chain breaks: 2 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "B" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 219 Unusual residues: {' NA': 1, 'C14': 3, 'CLR': 6, 'SIN': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 256 Unusual residues: {' NA': 1, '3PE': 2, 'C14': 3, 'CLR': 4, 'SIN': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 6.07, per 1000 atoms: 0.72 Number of scatterers: 8373 At special positions: 0 Unit cell: (88.275, 106.425, 84.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 2 15.00 Na 2 11.00 O 1339 8.00 N 1249 7.00 C 5730 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: 2.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.566A pdb=" N ALA B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 34 Proline residue: B 24 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.735A pdb=" N PHE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.836A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 86 removed outlier: 3.539A pdb=" N PHE B 86 " --> pdb=" O PRO B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 87 through 106 removed outlier: 3.581A pdb=" N TRP B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.632A pdb=" N ARG B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 143 through 163 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 225 through 246 removed outlier: 4.686A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.861A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 301 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 320 through 336 removed outlier: 3.547A pdb=" N GLY B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.660A pdb=" N THR B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 4.093A pdb=" N PHE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 426 through 446 removed outlier: 3.573A pdb=" N ILE B 430 " --> pdb=" O PRO B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 483 through 502 Proline residue: B 493 - end of helix removed outlier: 3.621A pdb=" N ILE B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 Proline residue: B 512 - end of helix Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 540 through 566 removed outlier: 4.008A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 14 through 28 Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.972A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.891A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.552A pdb=" N PHE A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.577A pdb=" N TRP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.710A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 143 through 163 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 220 through 247 removed outlier: 3.973A pdb=" N ASP A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.853A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 4.004A pdb=" N LEU A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 339 through 359 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 389 removed outlier: 3.822A pdb=" N ILE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.228A pdb=" N PHE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 502 Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 506 through 517 Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 540 through 566 removed outlier: 4.035A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 532 hydrogen bonds defined for protein. 1578 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: 2.26 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1240 1.32 - 1.44: 2204 1.44 - 1.57: 5084 1.57 - 1.69: 4 1.69 - 1.81: 88 Bond restraints: 8620 Sorted by residual: bond pdb=" C11 3PE A 705 " pdb=" O13 3PE A 705 " ideal model delta sigma weight residual 1.408 1.457 -0.049 2.00e-02 2.50e+03 5.94e+00 bond pdb=" C1 3PE A 709 " pdb=" O11 3PE A 709 " ideal model delta sigma weight residual 1.409 1.457 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C11 3PE A 709 " pdb=" O13 3PE A 709 " ideal model delta sigma weight residual 1.408 1.456 -0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" O13 3PE A 709 " pdb=" P 3PE A 709 " ideal model delta sigma weight residual 1.654 1.607 0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" O13 3PE A 705 " pdb=" P 3PE A 705 " ideal model delta sigma weight residual 1.654 1.608 0.046 2.00e-02 2.50e+03 5.38e+00 ... (remaining 8615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 11556 2.12 - 4.24: 168 4.24 - 6.36: 31 6.36 - 8.48: 2 8.48 - 10.60: 1 Bond angle restraints: 11758 Sorted by residual: angle pdb=" CB MET B 131 " pdb=" CG MET B 131 " pdb=" SD MET B 131 " ideal model delta sigma weight residual 112.70 102.10 10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C TYR B 85 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " ideal model delta sigma weight residual 122.62 118.63 3.99 1.63e+00 3.76e-01 6.01e+00 angle pdb=" C ILE B 364 " pdb=" CA ILE B 364 " pdb=" CB ILE B 364 " ideal model delta sigma weight residual 110.13 112.22 -2.09 9.70e-01 1.06e+00 4.65e+00 angle pdb=" C VAL B 425 " pdb=" N PRO B 426 " pdb=" CA PRO B 426 " ideal model delta sigma weight residual 119.84 122.47 -2.63 1.25e+00 6.40e-01 4.43e+00 angle pdb=" C VAL A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 119.84 122.46 -2.62 1.25e+00 6.40e-01 4.40e+00 ... (remaining 11753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 5247 24.30 - 48.60: 254 48.60 - 72.90: 39 72.90 - 97.19: 7 97.19 - 121.49: 7 Dihedral angle restraints: 5554 sinusoidal: 2644 harmonic: 2910 Sorted by residual: dihedral pdb=" CA PHE A 363 " pdb=" C PHE A 363 " pdb=" N ILE A 364 " pdb=" CA ILE A 364 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N LEU A 87 " pdb=" CA LEU A 87 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C10 CLR A 710 " pdb=" C1 CLR A 710 " pdb=" C2 CLR A 710 " pdb=" C3 CLR A 710 " ideal model delta sinusoidal sigma weight residual -56.83 64.66 -121.49 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 5551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 993 0.039 - 0.079: 295 0.079 - 0.118: 81 0.118 - 0.157: 15 0.157 - 0.196: 2 Chirality restraints: 1386 Sorted by residual: chirality pdb=" C2 3PE A 705 " pdb=" C1 3PE A 705 " pdb=" C3 3PE A 705 " pdb=" O21 3PE A 705 " both_signs ideal model delta sigma weight residual False -2.53 -2.33 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" C2 3PE A 709 " pdb=" C1 3PE A 709 " pdb=" C3 3PE A 709 " pdb=" O21 3PE A 709 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA MET B 131 " pdb=" N MET B 131 " pdb=" C MET B 131 " pdb=" CB MET B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1383 not shown) Planarity restraints: 1361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 152 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 153 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 528 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO B 529 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 529 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 529 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 86 " 0.020 2.00e-02 2.50e+03 1.79e-02 5.59e+00 pdb=" CG PHE B 86 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 86 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 86 " 0.002 2.00e-02 2.50e+03 ... (remaining 1358 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1480 2.76 - 3.30: 8227 3.30 - 3.83: 14518 3.83 - 4.37: 17236 4.37 - 4.90: 29649 Nonbonded interactions: 71110 Sorted by model distance: nonbonded pdb=" O ALA B 63 " pdb=" OH TYR B 85 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLU B 480 " pdb=" N MET B 522 " model vdw 2.257 3.120 nonbonded pdb=" O LEU A 561 " pdb=" OG1 THR A 565 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A 240 " pdb=" O PHE A 521 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 240 " pdb=" O PHE B 521 " model vdw 2.275 3.040 ... (remaining 71105 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 6 through 219 or resid 225 through 303 or resid 319 throug \ h 576 or resid 701 through 704 or resid 706 through 708)) selection = (chain 'B' and (resid 6 through 576 or resid 701 through 704 or resid 706 throug \ h 708)) } 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: 1.760 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:15.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.004 0.049 8620 Z= 0.251 Angle : 0.623 10.604 11758 Z= 0.293 Chirality : 0.041 0.196 1386 Planarity : 0.006 0.082 1361 Dihedral : 14.477 121.493 3662 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.23 (0.28), residues: 998 helix: 1.88 (0.20), residues: 765 sheet: None (None), residues: 0 loop : 0.29 (0.45), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 231 HIS 0.004 0.001 HIS A 109 PHE 0.041 0.001 PHE B 86 TYR 0.017 0.001 TYR B 508 ARG 0.005 0.000 ARG B 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.940 Fit side-chains REVERT: B 118 MET cc_start: 0.8172 (mtt) cc_final: 0.7870 (mtm) REVERT: B 231 TRP cc_start: 0.5846 (m100) cc_final: 0.5072 (m-90) REVERT: B 508 TYR cc_start: 0.7499 (t80) cc_final: 0.7045 (t80) REVERT: A 228 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7047 (mtm110) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 1.1049 time to fit residues: 167.7976 Evaluate side-chains 118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.0060 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 HIS A 552 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8620 Z= 0.211 Angle : 0.591 8.309 11758 Z= 0.282 Chirality : 0.041 0.162 1386 Planarity : 0.006 0.072 1361 Dihedral : 9.039 84.955 1866 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.24 % Allowed : 8.14 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.28), residues: 998 helix: 1.94 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.48 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 231 HIS 0.008 0.001 HIS B 457 PHE 0.017 0.001 PHE B 86 TYR 0.014 0.001 TYR B 508 ARG 0.005 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.889 Fit side-chains REVERT: B 413 GLU cc_start: 0.7381 (tp30) cc_final: 0.7115 (tp30) REVERT: B 508 TYR cc_start: 0.7467 (t80) cc_final: 0.6978 (t80) REVERT: A 228 ARG cc_start: 0.7447 (mtm180) cc_final: 0.7194 (mtm110) REVERT: A 572 GLN cc_start: 0.7946 (mm110) cc_final: 0.7628 (mm110) outliers start: 19 outliers final: 8 residues processed: 136 average time/residue: 1.0510 time to fit residues: 154.2417 Evaluate side-chains 129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.0060 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.7974 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8620 Z= 0.178 Angle : 0.540 6.628 11758 Z= 0.261 Chirality : 0.039 0.187 1386 Planarity : 0.006 0.071 1361 Dihedral : 8.596 86.752 1866 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.36 % Allowed : 10.61 % Favored : 87.03 % 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: 2.52 (0.28), residues: 998 helix: 2.02 (0.19), residues: 773 sheet: None (None), residues: 0 loop : 0.60 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 231 HIS 0.007 0.001 HIS B 457 PHE 0.015 0.001 PHE A 352 TYR 0.010 0.001 TYR B 508 ARG 0.005 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.932 Fit side-chains REVERT: B 413 GLU cc_start: 0.7355 (tp30) cc_final: 0.7094 (tp30) REVERT: B 508 TYR cc_start: 0.7464 (t80) cc_final: 0.6936 (t80) REVERT: A 48 MET cc_start: 0.9078 (mtp) cc_final: 0.8832 (mtm) REVERT: A 228 ARG cc_start: 0.7431 (mtm180) cc_final: 0.7173 (mtm110) outliers start: 20 outliers final: 7 residues processed: 138 average time/residue: 0.9456 time to fit residues: 141.5677 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8620 Z= 0.214 Angle : 0.546 6.109 11758 Z= 0.266 Chirality : 0.040 0.202 1386 Planarity : 0.006 0.069 1361 Dihedral : 8.563 87.697 1866 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.95 % Allowed : 11.56 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.28), residues: 998 helix: 2.04 (0.19), residues: 773 sheet: None (None), residues: 0 loop : 0.62 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 231 HIS 0.007 0.001 HIS B 457 PHE 0.017 0.001 PHE A 352 TYR 0.011 0.001 TYR B 508 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.854 Fit side-chains REVERT: B 413 GLU cc_start: 0.7359 (tp30) cc_final: 0.7118 (tp30) REVERT: B 508 TYR cc_start: 0.7440 (t80) cc_final: 0.6910 (t80) REVERT: A 445 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 25 outliers final: 11 residues processed: 139 average time/residue: 0.9337 time to fit residues: 140.8707 Evaluate side-chains 129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8620 Z= 0.242 Angle : 0.565 7.723 11758 Z= 0.275 Chirality : 0.041 0.223 1386 Planarity : 0.006 0.069 1361 Dihedral : 8.603 89.556 1866 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.95 % Allowed : 12.50 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.28), residues: 998 helix: 2.01 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.58 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 231 HIS 0.007 0.001 HIS B 457 PHE 0.018 0.001 PHE A 352 TYR 0.013 0.001 TYR B 508 ARG 0.004 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.970 Fit side-chains REVERT: B 86 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7471 (t80) REVERT: B 413 GLU cc_start: 0.7319 (tp30) cc_final: 0.7104 (tp30) REVERT: B 508 TYR cc_start: 0.7457 (t80) cc_final: 0.6919 (OUTLIER) REVERT: A 48 MET cc_start: 0.9096 (mtp) cc_final: 0.8862 (mtm) REVERT: A 228 ARG cc_start: 0.7278 (mtm110) cc_final: 0.7013 (mpp80) REVERT: A 445 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7506 (mm-30) outliers start: 25 outliers final: 18 residues processed: 135 average time/residue: 0.9059 time to fit residues: 133.3253 Evaluate side-chains 138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS A 552 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8620 Z= 0.192 Angle : 0.547 8.741 11758 Z= 0.266 Chirality : 0.040 0.251 1386 Planarity : 0.006 0.068 1361 Dihedral : 8.474 89.348 1866 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.07 % Allowed : 13.44 % Favored : 83.49 % 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: 2.63 (0.28), residues: 998 helix: 2.11 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.59 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 231 HIS 0.007 0.001 HIS B 457 PHE 0.016 0.001 PHE A 352 TYR 0.011 0.001 TYR B 508 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.045 Fit side-chains REVERT: B 86 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7291 (t80) REVERT: B 508 TYR cc_start: 0.7461 (t80) cc_final: 0.6844 (t80) REVERT: A 228 ARG cc_start: 0.7300 (mtm110) cc_final: 0.7022 (mpp80) REVERT: A 445 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7469 (mm-30) outliers start: 26 outliers final: 15 residues processed: 138 average time/residue: 0.9328 time to fit residues: 140.3049 Evaluate side-chains 132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8620 Z= 0.220 Angle : 0.564 9.542 11758 Z= 0.274 Chirality : 0.041 0.261 1386 Planarity : 0.006 0.068 1361 Dihedral : 8.557 88.542 1866 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.07 % Allowed : 13.80 % Favored : 83.14 % 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: 2.62 (0.28), residues: 998 helix: 2.10 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.58 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 231 HIS 0.009 0.001 HIS B 457 PHE 0.017 0.001 PHE A 352 TYR 0.011 0.001 TYR B 508 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.906 Fit side-chains REVERT: B 86 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7295 (t80) REVERT: B 105 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: B 118 MET cc_start: 0.7867 (mtp) cc_final: 0.7413 (mtp) REVERT: B 508 TYR cc_start: 0.7499 (t80) cc_final: 0.6386 (t80) REVERT: A 150 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8082 (tmm) REVERT: A 228 ARG cc_start: 0.7312 (mtm110) cc_final: 0.7017 (mpp80) REVERT: A 445 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 553 LEU cc_start: 0.8231 (mt) cc_final: 0.7807 (tt) outliers start: 26 outliers final: 16 residues processed: 139 average time/residue: 0.9464 time to fit residues: 143.2103 Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8620 Z= 0.197 Angle : 0.555 10.309 11758 Z= 0.272 Chirality : 0.041 0.281 1386 Planarity : 0.006 0.067 1361 Dihedral : 8.498 87.716 1866 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.95 % Allowed : 14.27 % Favored : 82.78 % 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: 2.67 (0.28), residues: 998 helix: 2.14 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.61 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 231 HIS 0.007 0.001 HIS B 457 PHE 0.017 0.001 PHE A 403 TYR 0.015 0.001 TYR B 508 ARG 0.005 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.882 Fit side-chains REVERT: B 86 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7277 (t80) REVERT: B 105 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: B 118 MET cc_start: 0.7824 (mtp) cc_final: 0.7356 (mtp) REVERT: A 150 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8099 (tmm) REVERT: A 228 ARG cc_start: 0.7272 (mtm110) cc_final: 0.6975 (mpp80) REVERT: A 553 LEU cc_start: 0.8193 (mt) cc_final: 0.7767 (tt) outliers start: 25 outliers final: 15 residues processed: 135 average time/residue: 0.8941 time to fit residues: 131.4396 Evaluate side-chains 138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8620 Z= 0.205 Angle : 0.566 11.131 11758 Z= 0.277 Chirality : 0.041 0.284 1386 Planarity : 0.006 0.067 1361 Dihedral : 8.517 87.042 1866 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.71 % Allowed : 14.98 % Favored : 82.31 % 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: 2.64 (0.28), residues: 998 helix: 2.12 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.60 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 231 HIS 0.008 0.001 HIS B 457 PHE 0.016 0.001 PHE A 352 TYR 0.015 0.001 TYR B 508 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.924 Fit side-chains REVERT: B 86 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7327 (t80) REVERT: B 105 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7803 (tp30) REVERT: B 118 MET cc_start: 0.7866 (mtp) cc_final: 0.7406 (mtp) REVERT: A 150 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8104 (tmm) REVERT: A 228 ARG cc_start: 0.7274 (mtm110) cc_final: 0.6966 (mpp80) REVERT: A 445 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7468 (mm-30) outliers start: 23 outliers final: 13 residues processed: 136 average time/residue: 0.9505 time to fit residues: 140.3461 Evaluate side-chains 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 99 optimal weight: 0.0570 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 24 optimal weight: 9.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8620 Z= 0.166 Angle : 0.546 10.986 11758 Z= 0.268 Chirality : 0.040 0.301 1386 Planarity : 0.006 0.068 1361 Dihedral : 8.267 86.270 1866 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.65 % Allowed : 16.16 % Favored : 82.19 % 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: 2.83 (0.28), residues: 998 helix: 2.27 (0.19), residues: 771 sheet: None (None), residues: 0 loop : 0.58 (0.46), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 231 HIS 0.008 0.001 HIS B 457 PHE 0.014 0.001 PHE A 352 TYR 0.013 0.001 TYR B 508 ARG 0.003 0.000 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.879 Fit side-chains REVERT: B 86 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 118 MET cc_start: 0.7778 (mtp) cc_final: 0.7300 (mtp) REVERT: B 119 LEU cc_start: 0.8753 (tp) cc_final: 0.8519 (mm) REVERT: B 231 TRP cc_start: 0.5975 (m100) cc_final: 0.5576 (t-100) REVERT: B 538 HIS cc_start: 0.7029 (m-70) cc_final: 0.6720 (m-70) REVERT: A 228 ARG cc_start: 0.7228 (mtm110) cc_final: 0.6932 (mpp80) REVERT: A 445 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7456 (mm-30) outliers start: 14 outliers final: 9 residues processed: 134 average time/residue: 0.9627 time to fit residues: 140.0898 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109306 restraints weight = 10963.857| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.03 r_work: 0.3277 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8620 Z= 0.213 Angle : 0.579 11.281 11758 Z= 0.284 Chirality : 0.041 0.287 1386 Planarity : 0.006 0.067 1361 Dihedral : 8.422 85.657 1866 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.65 % Allowed : 16.51 % Favored : 81.84 % 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: 2.75 (0.28), residues: 998 helix: 2.20 (0.19), residues: 770 sheet: None (None), residues: 0 loop : 0.65 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 231 HIS 0.010 0.001 HIS B 457 PHE 0.021 0.001 PHE A 403 TYR 0.016 0.001 TYR B 508 ARG 0.003 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.70 seconds wall clock time: 55 minutes 32.85 seconds (3332.85 seconds total)