Starting phenix.real_space_refine on Sat Jul 20 05:24:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/07_2024/6mgv_9112.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/07_2024/6mgv_9112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/07_2024/6mgv_9112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/07_2024/6mgv_9112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/07_2024/6mgv_9112.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/07_2024/6mgv_9112.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6744 2.51 5 N 1650 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 5.88, per 1000 atoms: 0.58 Number of scatterers: 10150 At special positions: 0 Unit cell: (123.05, 129.95, 95.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1708 8.00 N 1650 7.00 C 6744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 2 sheets defined 76.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Processing helix chain 'A' and resid 30 through 33 removed outlier: 6.322A pdb=" N PHE A 33 " --> pdb=" O LEU A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 33' Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.557A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 121 removed outlier: 4.048A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 195 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 314 through 317 removed outlier: 6.347A pdb=" N LYS A 317 " --> pdb=" O ASN A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.710A pdb=" N ILE A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 422 through 438 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 456 through 476 Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 504 through 512 Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 565 through 584 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 590 through 612 Processing helix chain 'A' and resid 623 through 646 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 659 through 677 Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.027A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 Processing helix chain 'B' and resid 30 through 33 removed outlier: 6.323A pdb=" N PHE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.557A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 121 removed outlier: 4.048A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 314 through 317 removed outlier: 6.347A pdb=" N LYS B 317 " --> pdb=" O ASN B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 317' Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 360 through 366 removed outlier: 3.711A pdb=" N ILE B 366 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 389 through 400 Processing helix chain 'B' and resid 422 through 438 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'B' and resid 456 through 476 Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 504 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 512 through 524 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 534 through 548 Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 565 through 584 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 590 through 612 Processing helix chain 'B' and resid 623 through 646 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 659 through 677 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.027A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.602A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.602A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 2055 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: 2.88 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2294 1.33 - 1.45: 2924 1.45 - 1.58: 5128 1.58 - 1.70: 6 1.70 - 1.83: 88 Bond restraints: 10440 Sorted by residual: bond pdb=" N PRO B 210 " pdb=" CD PRO B 210 " ideal model delta sigma weight residual 1.473 1.410 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" N PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 1.473 1.410 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CB GLN B 615 " pdb=" CG GLN B 615 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.43e+01 bond pdb=" CB GLN A 615 " pdb=" CG GLN A 615 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.43e+01 bond pdb=" N PRO A 715 " pdb=" CD PRO A 715 " ideal model delta sigma weight residual 1.473 1.424 0.049 1.40e-02 5.10e+03 1.21e+01 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.47: 301 105.47 - 112.69: 5188 112.69 - 119.91: 4279 119.91 - 127.13: 4313 127.13 - 134.35: 119 Bond angle restraints: 14200 Sorted by residual: angle pdb=" N SER B 619 " pdb=" CA SER B 619 " pdb=" C SER B 619 " ideal model delta sigma weight residual 110.17 98.84 11.33 1.61e+00 3.86e-01 4.95e+01 angle pdb=" N SER A 619 " pdb=" CA SER A 619 " pdb=" C SER A 619 " ideal model delta sigma weight residual 110.17 98.86 11.31 1.61e+00 3.86e-01 4.94e+01 angle pdb=" N ASP A 554 " pdb=" CA ASP A 554 " pdb=" C ASP A 554 " ideal model delta sigma weight residual 113.17 105.63 7.54 1.26e+00 6.30e-01 3.58e+01 angle pdb=" N ASP B 554 " pdb=" CA ASP B 554 " pdb=" C ASP B 554 " ideal model delta sigma weight residual 113.17 105.68 7.49 1.26e+00 6.30e-01 3.54e+01 angle pdb=" N LYS A 41 " pdb=" CA LYS A 41 " pdb=" C LYS A 41 " ideal model delta sigma weight residual 110.41 103.15 7.26 1.23e+00 6.61e-01 3.48e+01 ... (remaining 14195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 5849 14.74 - 29.49: 209 29.49 - 44.23: 38 44.23 - 58.98: 26 58.98 - 73.72: 6 Dihedral angle restraints: 6128 sinusoidal: 2386 harmonic: 3742 Sorted by residual: dihedral pdb=" CA ASP A 212 " pdb=" CB ASP A 212 " pdb=" CG ASP A 212 " pdb=" OD1 ASP A 212 " ideal model delta sinusoidal sigma weight residual -30.00 -82.32 52.32 1 2.00e+01 2.50e-03 9.33e+00 dihedral pdb=" CA ASP B 212 " pdb=" CB ASP B 212 " pdb=" CG ASP B 212 " pdb=" OD1 ASP B 212 " ideal model delta sinusoidal sigma weight residual -30.00 -82.29 52.29 1 2.00e+01 2.50e-03 9.32e+00 dihedral pdb=" N TYR A 613 " pdb=" C TYR A 613 " pdb=" CA TYR A 613 " pdb=" CB TYR A 613 " ideal model delta harmonic sigma weight residual 122.80 130.19 -7.39 0 2.50e+00 1.60e-01 8.74e+00 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1089 0.075 - 0.150: 401 0.150 - 0.225: 81 0.225 - 0.300: 28 0.300 - 0.375: 5 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA PHE A 109 " pdb=" N PHE A 109 " pdb=" C PHE A 109 " pdb=" CB PHE A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA PHE B 109 " pdb=" N PHE B 109 " pdb=" C PHE B 109 " pdb=" CB PHE B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA TYR A 613 " pdb=" N TYR A 613 " pdb=" C TYR A 613 " pdb=" CB TYR A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1601 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 352 " -0.041 2.00e-02 2.50e+03 1.98e-02 9.81e+00 pdb=" CG TRP B 352 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 352 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 352 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP B 352 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 352 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 352 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 352 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 352 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 352 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 519 " 0.036 2.00e-02 2.50e+03 2.20e-02 9.64e+00 pdb=" CG TYR A 519 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 519 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 519 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 519 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 519 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 519 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 519 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 352 " 0.040 2.00e-02 2.50e+03 1.96e-02 9.62e+00 pdb=" CG TRP A 352 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A 352 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 352 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 352 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 352 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 352 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 352 " 0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 352 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 352 " 0.019 2.00e-02 2.50e+03 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 192 2.65 - 3.21: 10310 3.21 - 3.77: 16551 3.77 - 4.34: 22521 4.34 - 4.90: 36727 Nonbonded interactions: 86301 Sorted by model distance: nonbonded pdb=" NH2 ARG B 330 " pdb=" OE1 GLU B 695 " model vdw 2.082 2.520 nonbonded pdb=" NH2 ARG A 330 " pdb=" OE1 GLU A 695 " model vdw 2.082 2.520 nonbonded pdb=" OH TYR A 167 " pdb=" O PHE A 657 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR B 167 " pdb=" O PHE B 657 " model vdw 2.212 2.440 nonbonded pdb=" NH1 ARG A 330 " pdb=" OE1 GLU A 695 " model vdw 2.272 2.520 ... (remaining 86296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.110 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.018 0.113 10440 Z= 1.176 Angle : 1.436 11.328 14200 Z= 0.968 Chirality : 0.084 0.375 1604 Planarity : 0.009 0.039 1762 Dihedral : 9.732 73.722 3696 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.37 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1248 helix: 0.35 (0.16), residues: 880 sheet: -1.04 (0.73), residues: 46 loop : -1.58 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.006 TRP B 352 HIS 0.011 0.003 HIS B 293 PHE 0.045 0.008 PHE A 72 TYR 0.045 0.009 TYR A 38 ARG 0.007 0.001 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.118 Fit side-chains REVERT: A 320 MET cc_start: 0.8368 (mmm) cc_final: 0.8164 (mmp) REVERT: A 638 SER cc_start: 0.8300 (t) cc_final: 0.8039 (p) REVERT: A 689 MET cc_start: 0.9055 (tpp) cc_final: 0.8805 (tpt) REVERT: B 320 MET cc_start: 0.8363 (mmm) cc_final: 0.8159 (mmp) REVERT: B 638 SER cc_start: 0.8302 (t) cc_final: 0.8039 (p) REVERT: B 689 MET cc_start: 0.9053 (tpp) cc_final: 0.8814 (tpt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2671 time to fit residues: 81.6129 Evaluate side-chains 163 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 341 GLN A 363 ASN A 607 HIS A 608 GLN A 614 ASN B 340 GLN B 341 GLN B 363 ASN B 607 HIS B 608 GLN B 614 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10440 Z= 0.229 Angle : 0.611 6.591 14200 Z= 0.328 Chirality : 0.044 0.154 1604 Planarity : 0.005 0.046 1762 Dihedral : 4.689 24.880 1360 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.57 % Allowed : 4.06 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1248 helix: 2.00 (0.17), residues: 844 sheet: -1.26 (0.77), residues: 42 loop : -1.37 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 624 HIS 0.004 0.001 HIS A 232 PHE 0.026 0.002 PHE A 428 TYR 0.012 0.002 TYR B 38 ARG 0.007 0.001 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 1.134 Fit side-chains REVERT: A 165 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6571 (mtp) REVERT: A 531 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: A 538 LEU cc_start: 0.8089 (tp) cc_final: 0.7852 (tp) REVERT: A 540 MET cc_start: 0.5561 (mmt) cc_final: 0.5354 (mmt) REVERT: A 559 MET cc_start: 0.7242 (ttp) cc_final: 0.6763 (ptm) REVERT: A 689 MET cc_start: 0.9062 (tpp) cc_final: 0.8855 (tpt) REVERT: B 165 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6588 (mtp) REVERT: B 531 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: B 538 LEU cc_start: 0.8086 (tp) cc_final: 0.7843 (tp) REVERT: B 540 MET cc_start: 0.5560 (mmt) cc_final: 0.5328 (mmt) REVERT: B 559 MET cc_start: 0.7247 (ttp) cc_final: 0.6758 (ptm) outliers start: 6 outliers final: 0 residues processed: 191 average time/residue: 0.2016 time to fit residues: 56.0453 Evaluate side-chains 155 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 531 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10440 Z= 0.191 Angle : 0.551 5.817 14200 Z= 0.292 Chirality : 0.041 0.140 1604 Planarity : 0.005 0.053 1762 Dihedral : 4.432 24.395 1360 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.13 % Allowed : 6.33 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1248 helix: 2.19 (0.17), residues: 844 sheet: -1.27 (0.74), residues: 46 loop : -1.70 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 624 HIS 0.003 0.001 HIS B 607 PHE 0.024 0.002 PHE A 428 TYR 0.009 0.001 TYR B 181 ARG 0.005 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.061 Fit side-chains REVERT: A 165 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6783 (mtp) REVERT: A 390 ILE cc_start: 0.8149 (mm) cc_final: 0.7761 (mm) REVERT: A 531 GLU cc_start: 0.6991 (mp0) cc_final: 0.6157 (mm-30) REVERT: A 540 MET cc_start: 0.5608 (mmt) cc_final: 0.5376 (mmt) REVERT: A 559 MET cc_start: 0.7248 (ttp) cc_final: 0.6800 (ptm) REVERT: A 645 LEU cc_start: 0.6669 (tt) cc_final: 0.6325 (tp) REVERT: B 165 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6792 (mtp) REVERT: B 390 ILE cc_start: 0.8141 (mm) cc_final: 0.7769 (mm) REVERT: B 531 GLU cc_start: 0.6988 (mp0) cc_final: 0.6155 (mm-30) REVERT: B 540 MET cc_start: 0.5612 (mmt) cc_final: 0.5354 (mmt) REVERT: B 559 MET cc_start: 0.7240 (ttp) cc_final: 0.6791 (ptm) REVERT: B 645 LEU cc_start: 0.6668 (tt) cc_final: 0.6323 (tp) outliers start: 12 outliers final: 4 residues processed: 169 average time/residue: 0.1913 time to fit residues: 47.3497 Evaluate side-chains 159 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 259 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS B 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10440 Z= 0.205 Angle : 0.544 6.161 14200 Z= 0.284 Chirality : 0.041 0.140 1604 Planarity : 0.005 0.054 1762 Dihedral : 4.364 24.840 1360 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.23 % Allowed : 8.13 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1248 helix: 2.23 (0.17), residues: 846 sheet: -1.33 (0.75), residues: 46 loop : -1.66 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 624 HIS 0.004 0.001 HIS A 670 PHE 0.023 0.002 PHE A 428 TYR 0.008 0.001 TYR A 181 ARG 0.004 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.035 Fit side-chains REVERT: A 165 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6839 (mtp) REVERT: A 531 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6295 (mt-10) REVERT: A 538 LEU cc_start: 0.8026 (tp) cc_final: 0.7820 (tp) REVERT: A 540 MET cc_start: 0.5583 (mmt) cc_final: 0.5344 (mmt) REVERT: A 559 MET cc_start: 0.7257 (ttp) cc_final: 0.6818 (ptm) REVERT: B 165 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6840 (mtp) REVERT: B 531 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6289 (mt-10) REVERT: B 538 LEU cc_start: 0.8014 (tp) cc_final: 0.7810 (tp) REVERT: B 540 MET cc_start: 0.5591 (mmt) cc_final: 0.5330 (mmt) REVERT: B 559 MET cc_start: 0.7249 (ttp) cc_final: 0.6809 (ptm) REVERT: B 645 LEU cc_start: 0.6539 (tt) cc_final: 0.6187 (tp) outliers start: 13 outliers final: 8 residues processed: 174 average time/residue: 0.1831 time to fit residues: 47.5026 Evaluate side-chains 175 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 643 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.0000 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10440 Z= 0.158 Angle : 0.521 6.837 14200 Z= 0.269 Chirality : 0.040 0.134 1604 Planarity : 0.004 0.053 1762 Dihedral : 4.163 23.788 1360 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.51 % Allowed : 9.17 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1248 helix: 2.37 (0.17), residues: 848 sheet: -1.48 (0.76), residues: 46 loop : -1.59 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 624 HIS 0.002 0.001 HIS A 670 PHE 0.025 0.001 PHE A 428 TYR 0.006 0.001 TYR A 43 ARG 0.003 0.000 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.137 Fit side-chains REVERT: A 388 PHE cc_start: 0.7273 (m-10) cc_final: 0.7069 (m-10) REVERT: A 531 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6100 (mm-30) REVERT: A 559 MET cc_start: 0.7240 (ttp) cc_final: 0.6819 (ptm) REVERT: A 564 ILE cc_start: 0.8601 (tp) cc_final: 0.8377 (tp) REVERT: A 645 LEU cc_start: 0.6520 (tt) cc_final: 0.6137 (tp) REVERT: B 388 PHE cc_start: 0.7338 (m-10) cc_final: 0.7095 (m-10) REVERT: B 531 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6101 (mm-30) REVERT: B 559 MET cc_start: 0.7232 (ttp) cc_final: 0.6801 (ptm) REVERT: B 564 ILE cc_start: 0.8614 (tp) cc_final: 0.8390 (tp) outliers start: 16 outliers final: 6 residues processed: 175 average time/residue: 0.1819 time to fit residues: 47.4770 Evaluate side-chains 174 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 643 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS B 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10440 Z= 0.175 Angle : 0.529 6.934 14200 Z= 0.270 Chirality : 0.041 0.159 1604 Planarity : 0.004 0.053 1762 Dihedral : 4.117 24.056 1360 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.23 % Allowed : 9.26 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1248 helix: 2.48 (0.17), residues: 834 sheet: -1.65 (0.73), residues: 46 loop : -1.46 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.003 0.001 HIS B 542 PHE 0.024 0.002 PHE B 428 TYR 0.007 0.001 TYR A 519 ARG 0.007 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 1.123 Fit side-chains REVERT: A 76 MET cc_start: 0.7858 (mtt) cc_final: 0.7372 (mtt) REVERT: A 388 PHE cc_start: 0.7265 (m-10) cc_final: 0.7055 (m-10) REVERT: A 531 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6130 (mm-30) REVERT: A 538 LEU cc_start: 0.8078 (tp) cc_final: 0.7865 (tp) REVERT: A 559 MET cc_start: 0.7227 (ttp) cc_final: 0.6868 (ptm) REVERT: A 564 ILE cc_start: 0.8639 (tp) cc_final: 0.8433 (tp) REVERT: B 76 MET cc_start: 0.7864 (mtt) cc_final: 0.7374 (mtt) REVERT: B 388 PHE cc_start: 0.7260 (m-10) cc_final: 0.7057 (m-10) REVERT: B 531 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6129 (mm-30) REVERT: B 559 MET cc_start: 0.7221 (ttp) cc_final: 0.6852 (ptm) REVERT: B 645 LEU cc_start: 0.6496 (tt) cc_final: 0.6106 (tp) outliers start: 13 outliers final: 6 residues processed: 179 average time/residue: 0.1802 time to fit residues: 48.3131 Evaluate side-chains 178 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 531 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 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 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10440 Z= 0.169 Angle : 0.522 8.051 14200 Z= 0.267 Chirality : 0.041 0.167 1604 Planarity : 0.004 0.053 1762 Dihedral : 4.032 23.164 1360 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.95 % Allowed : 10.11 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1248 helix: 2.42 (0.17), residues: 848 sheet: -1.66 (0.74), residues: 46 loop : -1.60 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.005 0.001 HIS A 542 PHE 0.026 0.001 PHE A 428 TYR 0.005 0.001 TYR B 469 ARG 0.007 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 1.158 Fit side-chains REVERT: A 76 MET cc_start: 0.7982 (mtt) cc_final: 0.7523 (mtt) REVERT: A 395 PHE cc_start: 0.6961 (m-10) cc_final: 0.6600 (m-10) REVERT: A 531 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6095 (mm-30) REVERT: B 76 MET cc_start: 0.7982 (mtt) cc_final: 0.7522 (mtt) REVERT: B 395 PHE cc_start: 0.6963 (m-10) cc_final: 0.6594 (m-10) REVERT: B 531 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6094 (mm-30) REVERT: B 538 LEU cc_start: 0.8032 (tp) cc_final: 0.7788 (tp) REVERT: B 559 MET cc_start: 0.7193 (ttp) cc_final: 0.6620 (ptm) REVERT: B 564 ILE cc_start: 0.8543 (tp) cc_final: 0.8126 (pt) outliers start: 10 outliers final: 8 residues processed: 174 average time/residue: 0.1872 time to fit residues: 48.7440 Evaluate side-chains 179 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 531 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10440 Z= 0.216 Angle : 0.553 9.699 14200 Z= 0.282 Chirality : 0.042 0.284 1604 Planarity : 0.005 0.053 1762 Dihedral : 4.095 23.149 1360 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.95 % Allowed : 10.59 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1248 helix: 2.44 (0.17), residues: 834 sheet: -1.74 (0.71), residues: 46 loop : -1.57 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.005 0.001 HIS A 542 PHE 0.024 0.002 PHE A 428 TYR 0.006 0.001 TYR B 469 ARG 0.008 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 1.186 Fit side-chains REVERT: A 76 MET cc_start: 0.7984 (mtt) cc_final: 0.7537 (mtt) REVERT: A 531 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6166 (mm-30) REVERT: A 538 LEU cc_start: 0.8020 (tp) cc_final: 0.7771 (tp) REVERT: B 76 MET cc_start: 0.7987 (mtt) cc_final: 0.7536 (mtt) REVERT: B 531 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6166 (mm-30) outliers start: 10 outliers final: 8 residues processed: 179 average time/residue: 0.1876 time to fit residues: 49.8139 Evaluate side-chains 185 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 531 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0030 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10440 Z= 0.236 Angle : 0.580 10.747 14200 Z= 0.292 Chirality : 0.044 0.322 1604 Planarity : 0.005 0.052 1762 Dihedral : 4.133 22.872 1360 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.23 % Allowed : 11.06 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1248 helix: 2.29 (0.17), residues: 848 sheet: -1.86 (0.69), residues: 46 loop : -1.67 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 624 HIS 0.006 0.001 HIS B 542 PHE 0.029 0.002 PHE B 382 TYR 0.007 0.001 TYR B 294 ARG 0.008 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 1.251 Fit side-chains REVERT: A 76 MET cc_start: 0.7900 (mtt) cc_final: 0.7446 (mtt) REVERT: A 395 PHE cc_start: 0.6967 (m-10) cc_final: 0.6647 (m-10) REVERT: A 436 LEU cc_start: 0.8498 (mt) cc_final: 0.8235 (mp) REVERT: A 531 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6201 (mm-30) REVERT: B 76 MET cc_start: 0.7922 (mtt) cc_final: 0.7481 (mtt) REVERT: B 395 PHE cc_start: 0.6749 (m-10) cc_final: 0.6442 (m-10) REVERT: B 531 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6197 (mm-30) outliers start: 13 outliers final: 8 residues processed: 180 average time/residue: 0.1864 time to fit residues: 50.0840 Evaluate side-chains 185 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 531 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0670 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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: 0.8016 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10440 Z= 0.163 Angle : 0.555 10.878 14200 Z= 0.277 Chirality : 0.042 0.303 1604 Planarity : 0.004 0.053 1762 Dihedral : 4.013 22.127 1360 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.04 % Allowed : 10.68 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1248 helix: 2.39 (0.17), residues: 846 sheet: -1.88 (0.71), residues: 46 loop : -1.81 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 624 HIS 0.007 0.001 HIS A 542 PHE 0.029 0.001 PHE A 428 TYR 0.007 0.001 TYR A 519 ARG 0.008 0.000 ARG A 698 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.051 Fit side-chains REVERT: A 76 MET cc_start: 0.7960 (mtt) cc_final: 0.7512 (mtt) REVERT: A 395 PHE cc_start: 0.6736 (m-10) cc_final: 0.6431 (m-10) REVERT: A 436 LEU cc_start: 0.8480 (mt) cc_final: 0.8232 (mp) REVERT: A 531 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6063 (mm-30) REVERT: B 76 MET cc_start: 0.7960 (mtt) cc_final: 0.7523 (mtt) REVERT: B 395 PHE cc_start: 0.6638 (m-10) cc_final: 0.6336 (m-10) REVERT: B 531 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6068 (mm-30) REVERT: B 564 ILE cc_start: 0.8576 (tp) cc_final: 0.8093 (pt) outliers start: 11 outliers final: 9 residues processed: 176 average time/residue: 0.1805 time to fit residues: 47.5728 Evaluate side-chains 186 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 531 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.159493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129172 restraints weight = 11804.189| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.47 r_work: 0.3192 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10440 Z= 0.181 Angle : 0.558 10.861 14200 Z= 0.279 Chirality : 0.043 0.308 1604 Planarity : 0.005 0.052 1762 Dihedral : 4.001 21.754 1360 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.13 % Allowed : 11.15 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1248 helix: 2.35 (0.17), residues: 848 sheet: -1.94 (0.70), residues: 46 loop : -1.84 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 624 HIS 0.005 0.001 HIS A 162 PHE 0.036 0.002 PHE A 437 TYR 0.007 0.001 TYR B 519 ARG 0.008 0.000 ARG A 698 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.94 seconds wall clock time: 41 minutes 11.30 seconds (2471.30 seconds total)