Starting phenix.real_space_refine on Sun May 11 17:39:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uve_42617/05_2025/8uve_42617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uve_42617/05_2025/8uve_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_42617/05_2025/8uve_42617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uve_42617/05_2025/8uve_42617.map" model { file = "/net/cci-nas-00/data/ceres_data/8uve_42617/05_2025/8uve_42617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uve_42617/05_2025/8uve_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-5687/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: 5.55, per 1000 atoms: 0.66 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: 2.34 Conformation dependent library (CDL) restraints added in 920.2 milliseconds 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: 0.73 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: 2.37 Time building geometry restraints manager: 2.67 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: 4.300 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.510 Find NCS groups from input model: 0.370 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:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.610 ------------------------------------------------------------------------------- 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= 0.182 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 Details of bonding type rmsd hydrogen bonds : bond 0.11269 ( 532) hydrogen bonds : angle 4.78880 ( 1578) covalent geometry : bond 0.00390 ( 8620) covalent geometry : angle 0.62268 (11758) *********************** 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 : 0.939 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: 1.0317 time to fit residues: 156.7978 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 : 0.898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112097 restraints weight = 10789.760| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.96 r_work: 0.3319 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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= 0.132 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 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 532) hydrogen bonds : angle 3.94604 ( 1578) covalent geometry : bond 0.00320 ( 8620) covalent geometry : angle 0.59139 (11758) *********************** 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 : 0.932 Fit side-chains REVERT: B 141 TRP cc_start: 0.6530 (m100) cc_final: 0.6329 (m100) REVERT: B 413 GLU cc_start: 0.7548 (tp30) cc_final: 0.7246 (tp30) REVERT: B 508 TYR cc_start: 0.7509 (t80) cc_final: 0.6977 (t80) REVERT: A 228 ARG cc_start: 0.7386 (mtm180) cc_final: 0.7151 (mtm110) REVERT: A 325 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7382 (mtm110) REVERT: A 572 GLN cc_start: 0.7937 (mm110) cc_final: 0.7613 (mm110) outliers start: 19 outliers final: 8 residues processed: 136 average time/residue: 1.0262 time to fit residues: 150.6593 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 : 0.880 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112103 restraints weight = 10953.829| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.97 r_work: 0.3320 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1270 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= 0.118 Angle : 0.544 6.639 11758 Z= 0.263 Chirality : 0.040 0.184 1386 Planarity : 0.006 0.070 1361 Dihedral : 8.634 86.747 1866 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.24 % Allowed : 10.50 % Favored : 87.26 % 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 : 0.59 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 16 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 532) hydrogen bonds : angle 3.79574 ( 1578) covalent geometry : bond 0.00284 ( 8620) covalent geometry : angle 0.54363 (11758) *********************** 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: 19 poor density : 126 time to evaluate : 0.847 Fit side-chains REVERT: B 413 GLU cc_start: 0.7527 (tp30) cc_final: 0.7215 (tp30) REVERT: B 508 TYR cc_start: 0.7529 (t80) cc_final: 0.6942 (t80) REVERT: A 228 ARG cc_start: 0.7354 (mtm180) cc_final: 0.7113 (mtm110) outliers start: 19 outliers final: 7 residues processed: 138 average time/residue: 0.8529 time to fit residues: 128.2512 Evaluate side-chains 126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 70 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112641 restraints weight = 10794.777| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.96 r_work: 0.3314 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8620 Z= 0.114 Angle : 0.529 5.977 11758 Z= 0.258 Chirality : 0.040 0.206 1386 Planarity : 0.006 0.070 1361 Dihedral : 8.434 87.682 1866 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.71 % Allowed : 11.32 % Favored : 85.97 % 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: 2.63 (0.28), residues: 998 helix: 2.09 (0.19), residues: 773 sheet: None (None), residues: 0 loop : 0.64 (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 0.015 0.001 PHE A 352 TYR 0.010 0.001 TYR B 508 ARG 0.005 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 532) hydrogen bonds : angle 3.73553 ( 1578) covalent geometry : bond 0.00275 ( 8620) covalent geometry : angle 0.52926 (11758) *********************** 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 147 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.929 Fit side-chains REVERT: B 413 GLU cc_start: 0.7557 (tp30) cc_final: 0.7258 (tp30) REVERT: B 508 TYR cc_start: 0.7429 (t80) cc_final: 0.6822 (t80) REVERT: A 228 ARG cc_start: 0.7331 (mtm180) cc_final: 0.7093 (mtm110) REVERT: A 325 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7402 (mtm110) REVERT: A 445 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7675 (mm-30) outliers start: 23 outliers final: 9 residues processed: 140 average time/residue: 0.8787 time to fit residues: 133.9431 Evaluate side-chains 127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 74 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110366 restraints weight = 10794.895| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.94 r_work: 0.3302 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8620 Z= 0.140 Angle : 0.557 7.638 11758 Z= 0.272 Chirality : 0.041 0.216 1386 Planarity : 0.006 0.069 1361 Dihedral : 8.481 89.164 1866 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.83 % Allowed : 12.03 % Favored : 85.14 % 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: 2.60 (0.28), residues: 998 helix: 2.09 (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 0.024 0.001 TRP B 231 HIS 0.007 0.001 HIS B 457 PHE 0.017 0.001 PHE A 352 TYR 0.012 0.001 TYR B 508 ARG 0.004 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 532) hydrogen bonds : angle 3.81760 ( 1578) covalent geometry : bond 0.00349 ( 8620) covalent geometry : angle 0.55729 (11758) *********************** 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 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.839 Fit side-chains REVERT: B 86 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7459 (t80) REVERT: B 119 LEU cc_start: 0.8664 (tp) cc_final: 0.8398 (mm) REVERT: B 413 GLU cc_start: 0.7511 (tp30) cc_final: 0.7235 (tp30) REVERT: B 508 TYR cc_start: 0.7498 (t80) cc_final: 0.6892 (t80) REVERT: A 445 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 553 LEU cc_start: 0.7961 (mt) cc_final: 0.7546 (tt) outliers start: 24 outliers final: 14 residues processed: 137 average time/residue: 0.8905 time to fit residues: 132.4782 Evaluate side-chains 136 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 399 LEU 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 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 96 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110330 restraints weight = 10844.440| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.04 r_work: 0.3264 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1593 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= 0.130 Angle : 0.550 8.542 11758 Z= 0.268 Chirality : 0.040 0.249 1386 Planarity : 0.006 0.068 1361 Dihedral : 8.461 89.685 1866 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.95 % Allowed : 13.44 % Favored : 83.61 % 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: 2.65 (0.28), residues: 998 helix: 2.13 (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 0.016 0.001 PHE A 352 TYR 0.011 0.001 TYR B 508 ARG 0.004 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 532) hydrogen bonds : angle 3.77553 ( 1578) covalent geometry : bond 0.00320 ( 8620) covalent geometry : angle 0.55030 (11758) *********************** 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: 25 poor density : 123 time to evaluate : 0.914 Fit side-chains REVERT: B 86 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7232 (t80) REVERT: B 119 LEU cc_start: 0.8579 (tp) cc_final: 0.8309 (mm) REVERT: B 413 GLU cc_start: 0.7484 (tp30) cc_final: 0.7233 (tp30) REVERT: B 508 TYR cc_start: 0.7456 (t80) cc_final: 0.6805 (t80) REVERT: A 228 ARG cc_start: 0.7069 (mtm110) cc_final: 0.6820 (mpp80) REVERT: A 445 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7598 (mm-30) outliers start: 25 outliers final: 15 residues processed: 139 average time/residue: 0.9080 time to fit residues: 137.1618 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 : 0.894 ------------------------------------------------------------------------------- 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 386 VAL Chi-restraints excluded: chain B residue 466 LEU 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 549 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.147764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110514 restraints weight = 10904.717| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.04 r_work: 0.3268 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1666 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= 0.124 Angle : 0.554 9.353 11758 Z= 0.270 Chirality : 0.040 0.272 1386 Planarity : 0.006 0.068 1361 Dihedral : 8.433 88.869 1866 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.71 % Allowed : 14.15 % 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: 2.66 (0.28), residues: 998 helix: 2.13 (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 0.024 0.001 TRP B 231 HIS 0.007 0.001 HIS B 457 PHE 0.017 0.001 PHE A 403 TYR 0.010 0.001 TYR B 508 ARG 0.006 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 532) hydrogen bonds : angle 3.78205 ( 1578) covalent geometry : bond 0.00305 ( 8620) covalent geometry : angle 0.55380 (11758) *********************** 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 146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.899 Fit side-chains REVERT: B 86 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7137 (t80) REVERT: B 105 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: B 119 LEU cc_start: 0.8565 (tp) cc_final: 0.8301 (mm) REVERT: B 413 GLU cc_start: 0.7485 (tp30) cc_final: 0.7251 (tp30) REVERT: B 508 TYR cc_start: 0.7445 (t80) cc_final: 0.6342 (t80) REVERT: A 228 ARG cc_start: 0.7113 (mtm110) cc_final: 0.6879 (mpp80) REVERT: A 445 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 553 LEU cc_start: 0.7857 (mt) cc_final: 0.7462 (tt) outliers start: 23 outliers final: 13 residues processed: 140 average time/residue: 0.8981 time to fit residues: 136.4850 Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 523 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 86 PHE 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 469 LEU Chi-restraints excluded: chain A residue 527 THR 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 72 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.144903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107343 restraints weight = 10907.577| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.10 r_work: 0.3221 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8620 Z= 0.175 Angle : 0.606 9.717 11758 Z= 0.296 Chirality : 0.043 0.252 1386 Planarity : 0.006 0.068 1361 Dihedral : 8.881 87.997 1866 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.71 % Allowed : 14.62 % Favored : 82.67 % 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: 2.44 (0.28), residues: 998 helix: 1.97 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.52 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 231 HIS 0.010 0.001 HIS B 457 PHE 0.019 0.001 PHE A 352 TYR 0.014 0.001 TYR B 508 ARG 0.006 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 532) hydrogen bonds : angle 3.95090 ( 1578) covalent geometry : bond 0.00445 ( 8620) covalent geometry : angle 0.60629 (11758) *********************** 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 143 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.912 Fit side-chains REVERT: B 86 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7318 (t80) REVERT: B 105 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: B 119 LEU cc_start: 0.8560 (tp) cc_final: 0.8281 (mm) REVERT: B 413 GLU cc_start: 0.7524 (tp30) cc_final: 0.7307 (tp30) REVERT: A 228 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6881 (mpp80) REVERT: A 445 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 553 LEU cc_start: 0.7803 (mt) cc_final: 0.7414 (tt) outliers start: 23 outliers final: 12 residues processed: 134 average time/residue: 0.8799 time to fit residues: 128.5161 Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 523 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 86 PHE 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 549 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 55 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110333 restraints weight = 11046.490| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.97 r_work: 0.3302 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1731 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= 0.131 Angle : 0.581 10.739 11758 Z= 0.286 Chirality : 0.041 0.272 1386 Planarity : 0.006 0.068 1361 Dihedral : 8.664 86.772 1866 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.59 % Allowed : 15.21 % 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: 2.53 (0.28), residues: 998 helix: 2.04 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.53 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 231 HIS 0.007 0.001 HIS B 457 PHE 0.019 0.001 PHE A 403 TYR 0.012 0.001 TYR B 508 ARG 0.005 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 532) hydrogen bonds : angle 3.88603 ( 1578) covalent geometry : bond 0.00321 ( 8620) covalent geometry : angle 0.58128 (11758) *********************** 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 144 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.912 Fit side-chains REVERT: B 86 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7240 (t80) REVERT: B 105 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: B 119 LEU cc_start: 0.8626 (tp) cc_final: 0.8385 (mm) REVERT: B 413 GLU cc_start: 0.7578 (tp30) cc_final: 0.7370 (tp30) REVERT: A 228 ARG cc_start: 0.7181 (mtm110) cc_final: 0.6925 (mpp80) REVERT: A 445 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7673 (mm-30) outliers start: 22 outliers final: 12 residues processed: 136 average time/residue: 0.8869 time to fit residues: 131.3716 Evaluate side-chains 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 523 LEU Chi-restraints excluded: chain A residue 86 PHE 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 4 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111124 restraints weight = 10843.821| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.04 r_work: 0.3266 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8620 Z= 0.124 Angle : 0.580 11.010 11758 Z= 0.286 Chirality : 0.041 0.299 1386 Planarity : 0.006 0.067 1361 Dihedral : 8.534 86.134 1866 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.00 % Allowed : 15.68 % 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: 2.63 (0.28), residues: 998 helix: 2.10 (0.19), residues: 771 sheet: None (None), residues: 0 loop : 0.64 (0.46), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 231 HIS 0.009 0.001 HIS B 457 PHE 0.015 0.001 PHE A 352 TYR 0.012 0.001 TYR B 240 ARG 0.005 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 532) hydrogen bonds : angle 3.91239 ( 1578) covalent geometry : bond 0.00305 ( 8620) covalent geometry : angle 0.57969 (11758) ********************** 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 142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.827 Fit side-chains REVERT: B 86 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7196 (t80) REVERT: B 105 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: B 119 LEU cc_start: 0.8511 (tp) cc_final: 0.8245 (mm) REVERT: B 413 GLU cc_start: 0.7496 (tp30) cc_final: 0.7278 (tp30) REVERT: B 508 TYR cc_start: 0.7336 (t80) cc_final: 0.6239 (t80) REVERT: A 228 ARG cc_start: 0.7087 (mtm110) cc_final: 0.6842 (mpp80) REVERT: A 445 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7593 (mm-30) outliers start: 17 outliers final: 12 residues processed: 137 average time/residue: 0.8661 time to fit residues: 129.3003 Evaluate side-chains 134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 523 LEU Chi-restraints excluded: chain A residue 86 PHE 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 31 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 84 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112144 restraints weight = 10909.860| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.06 r_work: 0.3285 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8620 Z= 0.117 Angle : 0.572 11.516 11758 Z= 0.283 Chirality : 0.041 0.299 1386 Planarity : 0.006 0.067 1361 Dihedral : 8.406 85.483 1866 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.53 % Allowed : 15.92 % Favored : 82.55 % 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: 2.71 (0.28), residues: 998 helix: 2.17 (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 0.032 0.001 TRP B 231 HIS 0.006 0.001 HIS B 457 PHE 0.015 0.001 PHE A 352 TYR 0.015 0.001 TYR B 240 ARG 0.005 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 532) hydrogen bonds : angle 3.88352 ( 1578) covalent geometry : bond 0.00285 ( 8620) covalent geometry : angle 0.57165 (11758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6180.28 seconds wall clock time: 107 minutes 4.06 seconds (6424.06 seconds total)