Starting phenix.real_space_refine on Tue Feb 13 20:43:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/02_2024/8emr_28262.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/02_2024/8emr_28262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/02_2024/8emr_28262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/02_2024/8emr_28262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/02_2024/8emr_28262.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/02_2024/8emr_28262.pdb" } resolution = 2.92 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= 0.030 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 35 5.16 5 C 4880 2.51 5 N 1329 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7685 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6930 Classifications: {'peptide': 859} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 798} Chain breaks: 2 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 703 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.69, per 1000 atoms: 0.61 Number of scatterers: 7685 At special positions: 0 Unit cell: (70.2, 87.48, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 35 16.00 O 1439 8.00 N 1329 7.00 C 4880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 116 " distance=2.03 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A 97 " Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 22.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.530A pdb=" N ASN A 37 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.873A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.662A pdb=" N LYS A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.900A pdb=" N GLU A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.674A pdb=" N ARG A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 4.580A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.661A pdb=" N ASP A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.434A pdb=" N GLN A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.804A pdb=" N ASN A 741 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 742 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.572A pdb=" N THR A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 10.464A pdb=" N LEU A 64 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N ILE A 79 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 66 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 77 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 93 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 10.464A pdb=" N LEU A 64 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N ILE A 79 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 66 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 77 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS A 255 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 139 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG A 133 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 139 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG A 133 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 540 removed outlier: 7.299A pdb=" N HIS A 397 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.876A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AA9, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.081A pdb=" N ILE A 828 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 891 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TRP A 888 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY A 932 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU A 890 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 839 through 846 Processing sheet with id=AB2, first strand: chain 'B' and resid 74 through 76 277 hydrogen bonds defined for protein. 732 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: 2.93 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1278 1.32 - 1.44: 2277 1.44 - 1.57: 4299 1.57 - 1.69: 0 1.69 - 1.82: 53 Bond restraints: 7907 Sorted by residual: bond pdb=" CA ARG A 818 " pdb=" C ARG A 818 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.30e-02 5.92e+03 4.02e+01 bond pdb=" C ARG A 817 " pdb=" N ARG A 818 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA SER A 819 " pdb=" C SER A 819 " ideal model delta sigma weight residual 1.525 1.459 0.066 1.25e-02 6.40e+03 2.82e+01 bond pdb=" C SER A 819 " pdb=" O SER A 819 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.08e-02 8.57e+03 1.64e+01 bond pdb=" C ARG A 818 " pdb=" O ARG A 818 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.17e-02 7.31e+03 1.51e+01 ... (remaining 7902 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.09: 343 107.09 - 113.85: 4230 113.85 - 120.60: 3083 120.60 - 127.35: 2979 127.35 - 134.11: 133 Bond angle restraints: 10768 Sorted by residual: angle pdb=" N GLY A 612 " pdb=" CA GLY A 612 " pdb=" C GLY A 612 " ideal model delta sigma weight residual 110.20 115.31 -5.11 1.32e+00 5.74e-01 1.50e+01 angle pdb=" N ARG A 817 " pdb=" CA ARG A 817 " pdb=" C ARG A 817 " ideal model delta sigma weight residual 109.41 103.74 5.67 1.52e+00 4.33e-01 1.39e+01 angle pdb=" C ARG A 817 " pdb=" N ARG A 818 " pdb=" CA ARG A 818 " ideal model delta sigma weight residual 120.28 125.13 -4.85 1.34e+00 5.57e-01 1.31e+01 angle pdb=" C MET A 814 " pdb=" N ARG A 815 " pdb=" CA ARG A 815 " ideal model delta sigma weight residual 123.05 118.19 4.86 1.40e+00 5.10e-01 1.20e+01 angle pdb=" CA ARG A 817 " pdb=" C ARG A 817 " pdb=" N ARG A 818 " ideal model delta sigma weight residual 115.42 121.07 -5.65 1.64e+00 3.72e-01 1.19e+01 ... (remaining 10763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 4394 21.81 - 43.62: 277 43.62 - 65.43: 24 65.43 - 87.24: 14 87.24 - 109.05: 9 Dihedral angle restraints: 4718 sinusoidal: 1972 harmonic: 2746 Sorted by residual: dihedral pdb=" CB CYS B 100 " pdb=" SG CYS B 100 " pdb=" SG CYS B 116 " pdb=" CB CYS B 116 " ideal model delta sinusoidal sigma weight residual -86.00 -156.29 70.29 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS B 77 " pdb=" SG CYS B 77 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 60.24 32.76 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" C MET A 814 " pdb=" N MET A 814 " pdb=" CA MET A 814 " pdb=" CB MET A 814 " ideal model delta harmonic sigma weight residual -122.60 -132.11 9.51 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1066 0.090 - 0.181: 75 0.181 - 0.271: 0 0.271 - 0.362: 1 0.362 - 0.452: 1 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA MET A 814 " pdb=" N MET A 814 " pdb=" C MET A 814 " pdb=" CB MET A 814 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TRP A 503 " pdb=" N TRP A 503 " pdb=" C TRP A 503 " pdb=" CB TRP A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 1140 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 489 " 0.020 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR A 489 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 489 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 489 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 489 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 489 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 489 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 489 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 87 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO B 88 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 306 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 307 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.023 5.00e-02 4.00e+02 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1713 2.79 - 3.32: 6617 3.32 - 3.84: 12673 3.84 - 4.37: 15067 4.37 - 4.90: 26466 Nonbonded interactions: 62536 Sorted by model distance: nonbonded pdb=" OH TYR A 257 " pdb=" O PHE A 740 " model vdw 2.263 2.440 nonbonded pdb=" O ARG B 91 " pdb="CA CA B 601 " model vdw 2.275 2.510 nonbonded pdb=" OD2 ASP A 848 " pdb=" OG1 THR A 851 " model vdw 2.284 2.440 nonbonded pdb=" O VAL B 96 " pdb="CA CA B 601 " model vdw 2.303 2.510 nonbonded pdb=" OD2 ASP B 104 " pdb="CA CA B 601 " model vdw 2.316 2.510 ... (remaining 62531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.000 Extract box with map and model: 5.970 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.200 Find NCS groups from input model: 0.210 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: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 7907 Z= 0.226 Angle : 0.624 7.221 10768 Z= 0.331 Chirality : 0.046 0.452 1143 Planarity : 0.005 0.046 1412 Dihedral : 14.915 109.049 2948 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.58 (0.27), residues: 944 helix: 1.26 (0.42), residues: 153 sheet: 0.46 (0.36), residues: 241 loop : -1.32 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 503 HIS 0.004 0.001 HIS A 480 PHE 0.014 0.001 PHE A 673 TYR 0.042 0.001 TYR A 489 ARG 0.004 0.000 ARG A 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.942 Fit side-chains REVERT: A 416 PHE cc_start: 0.7537 (m-80) cc_final: 0.7329 (m-10) REVERT: A 524 MET cc_start: 0.8008 (tpp) cc_final: 0.7781 (tpp) REVERT: A 543 MET cc_start: 0.8380 (mtp) cc_final: 0.8090 (mtp) REVERT: A 699 ASP cc_start: 0.8455 (t0) cc_final: 0.8222 (t0) REVERT: A 882 HIS cc_start: 0.7791 (m-70) cc_final: 0.6588 (p90) REVERT: A 908 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8086 (mmmt) REVERT: A 942 HIS cc_start: 0.6925 (m-70) cc_final: 0.6307 (t-90) REVERT: B 63 ASP cc_start: 0.6869 (p0) cc_final: 0.6656 (p0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 1.1530 time to fit residues: 161.8880 Evaluate side-chains 85 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 676 HIS A 741 ASN A 841 GLN A 853 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7907 Z= 0.323 Angle : 0.621 6.803 10768 Z= 0.311 Chirality : 0.046 0.164 1143 Planarity : 0.005 0.046 1412 Dihedral : 9.232 71.019 1132 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.13 % Allowed : 9.16 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.52 (0.28), residues: 944 helix: 1.64 (0.44), residues: 155 sheet: 0.31 (0.35), residues: 249 loop : -1.31 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 501 HIS 0.007 0.002 HIS A 77 PHE 0.011 0.001 PHE B 48 TYR 0.014 0.001 TYR A 477 ARG 0.007 0.001 ARG A 817 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 0.922 Fit side-chains REVERT: A 107 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7708 (mp0) REVERT: A 154 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8180 (mtp-110) REVERT: A 416 PHE cc_start: 0.7639 (m-80) cc_final: 0.7333 (m-10) REVERT: A 489 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: A 561 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: A 699 ASP cc_start: 0.8492 (t0) cc_final: 0.8232 (t0) REVERT: A 882 HIS cc_start: 0.8065 (m-70) cc_final: 0.6531 (p90) REVERT: A 908 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8068 (mmmt) outliers start: 26 outliers final: 8 residues processed: 96 average time/residue: 1.2159 time to fit residues: 124.1614 Evaluate side-chains 84 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 624 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 676 HIS A 692 GLN B 76 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7907 Z= 0.358 Angle : 0.637 7.223 10768 Z= 0.318 Chirality : 0.047 0.163 1143 Planarity : 0.005 0.044 1412 Dihedral : 7.309 60.939 1132 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.49 % Allowed : 11.33 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 944 helix: 1.50 (0.43), residues: 154 sheet: 0.21 (0.35), residues: 245 loop : -1.47 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 540 HIS 0.005 0.002 HIS A 180 PHE 0.014 0.001 PHE B 48 TYR 0.013 0.002 TYR A 712 ARG 0.005 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 0.949 Fit side-chains REVERT: A 107 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7689 (mp0) REVERT: A 416 PHE cc_start: 0.7620 (m-80) cc_final: 0.7164 (m-10) REVERT: A 437 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5008 (mpt-90) REVERT: A 561 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: A 699 ASP cc_start: 0.8485 (t0) cc_final: 0.8211 (t0) REVERT: A 841 GLN cc_start: 0.8499 (tt0) cc_final: 0.8226 (tt0) REVERT: A 882 HIS cc_start: 0.8259 (m-70) cc_final: 0.6543 (p90) REVERT: A 908 LYS cc_start: 0.8408 (mmtm) cc_final: 0.8045 (mmmt) REVERT: B 56 CYS cc_start: 0.7766 (t) cc_final: 0.7487 (t) outliers start: 29 outliers final: 13 residues processed: 96 average time/residue: 1.2082 time to fit residues: 123.2336 Evaluate side-chains 85 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 857 ARG Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 HIS A 676 HIS A 692 GLN A 855 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7907 Z= 0.275 Angle : 0.595 7.278 10768 Z= 0.295 Chirality : 0.045 0.183 1143 Planarity : 0.005 0.042 1412 Dihedral : 6.344 51.752 1132 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.13 % Allowed : 13.61 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.70 (0.27), residues: 944 helix: 1.66 (0.44), residues: 154 sheet: 0.21 (0.35), residues: 246 loop : -1.49 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 501 HIS 0.004 0.001 HIS A 77 PHE 0.013 0.001 PHE B 48 TYR 0.011 0.001 TYR A 498 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 0.866 Fit side-chains REVERT: A 107 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7643 (mt-10) REVERT: A 253 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7630 (mtt) REVERT: A 324 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7978 (t0) REVERT: A 416 PHE cc_start: 0.7525 (m-80) cc_final: 0.7156 (m-10) REVERT: A 437 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.4833 (mpt-90) REVERT: A 478 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.5229 (ttp80) REVERT: A 561 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: A 699 ASP cc_start: 0.8473 (t0) cc_final: 0.8188 (t0) REVERT: A 841 GLN cc_start: 0.8494 (tt0) cc_final: 0.8234 (tt0) REVERT: A 882 HIS cc_start: 0.8298 (m-70) cc_final: 0.6517 (p90) REVERT: A 908 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8072 (mmmt) REVERT: B 54 ASP cc_start: 0.8031 (m-30) cc_final: 0.7638 (m-30) outliers start: 26 outliers final: 12 residues processed: 96 average time/residue: 1.2115 time to fit residues: 123.6090 Evaluate side-chains 92 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 793 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.0570 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 HIS A 692 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7907 Z= 0.217 Angle : 0.557 7.201 10768 Z= 0.275 Chirality : 0.044 0.172 1143 Planarity : 0.004 0.040 1412 Dihedral : 5.693 44.832 1132 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.01 % Allowed : 14.10 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.61 (0.27), residues: 944 helix: 1.86 (0.44), residues: 154 sheet: 0.24 (0.34), residues: 244 loop : -1.46 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 501 HIS 0.005 0.001 HIS A 678 PHE 0.011 0.001 PHE A 101 TYR 0.015 0.001 TYR A 498 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.848 Fit side-chains REVERT: A 107 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7727 (mt-10) REVERT: A 228 GLU cc_start: 0.6851 (mp0) cc_final: 0.6516 (mp0) REVERT: A 324 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7903 (t0) REVERT: A 416 PHE cc_start: 0.7495 (m-80) cc_final: 0.7131 (m-10) REVERT: A 437 ARG cc_start: 0.6040 (OUTLIER) cc_final: 0.4687 (mpt-90) REVERT: A 478 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.5176 (ttp80) REVERT: A 561 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: A 699 ASP cc_start: 0.8471 (t0) cc_final: 0.8180 (t0) REVERT: A 705 TYR cc_start: 0.8756 (m-80) cc_final: 0.8507 (m-10) REVERT: A 841 GLN cc_start: 0.8526 (tt0) cc_final: 0.8248 (tt0) REVERT: A 864 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8139 (ttm-80) REVERT: A 882 HIS cc_start: 0.8319 (m-70) cc_final: 0.6509 (p90) REVERT: A 908 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8110 (mmmt) REVERT: B 54 ASP cc_start: 0.7973 (m-30) cc_final: 0.7610 (m-30) outliers start: 25 outliers final: 12 residues processed: 98 average time/residue: 1.2936 time to fit residues: 134.3099 Evaluate side-chains 93 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 793 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7907 Z= 0.243 Angle : 0.573 7.779 10768 Z= 0.283 Chirality : 0.044 0.178 1143 Planarity : 0.004 0.040 1412 Dihedral : 5.362 43.739 1132 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.49 % Allowed : 16.27 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 944 helix: 1.84 (0.44), residues: 154 sheet: 0.15 (0.34), residues: 242 loop : -1.43 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 501 HIS 0.005 0.001 HIS A 678 PHE 0.013 0.001 PHE B 48 TYR 0.007 0.001 TYR A 477 ARG 0.003 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 0.892 Fit side-chains REVERT: A 107 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7701 (mt-10) REVERT: A 228 GLU cc_start: 0.6868 (mp0) cc_final: 0.6473 (mp0) REVERT: A 416 PHE cc_start: 0.7538 (m-80) cc_final: 0.7206 (m-10) REVERT: A 437 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.4601 (mpt-90) REVERT: A 478 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5230 (ttp80) REVERT: A 561 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: A 699 ASP cc_start: 0.8475 (t0) cc_final: 0.8183 (t0) REVERT: A 841 GLN cc_start: 0.8530 (tt0) cc_final: 0.8233 (tt0) REVERT: A 864 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8122 (ttm-80) REVERT: A 882 HIS cc_start: 0.8386 (m-70) cc_final: 0.6532 (p90) REVERT: A 908 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8081 (mmmt) REVERT: B 54 ASP cc_start: 0.7974 (m-30) cc_final: 0.7607 (m-30) outliers start: 29 outliers final: 16 residues processed: 96 average time/residue: 1.2377 time to fit residues: 126.0131 Evaluate side-chains 94 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7907 Z= 0.181 Angle : 0.536 6.893 10768 Z= 0.263 Chirality : 0.043 0.157 1143 Planarity : 0.004 0.040 1412 Dihedral : 5.004 41.125 1132 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.13 % Allowed : 16.99 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.53 (0.28), residues: 944 helix: 1.98 (0.44), residues: 154 sheet: 0.26 (0.35), residues: 237 loop : -1.39 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 687 HIS 0.005 0.001 HIS A 678 PHE 0.012 0.001 PHE A 101 TYR 0.009 0.001 TYR A 477 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.913 Fit side-chains REVERT: A 107 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7690 (mt-10) REVERT: A 228 GLU cc_start: 0.6852 (mp0) cc_final: 0.6443 (mp0) REVERT: A 416 PHE cc_start: 0.7483 (m-80) cc_final: 0.7185 (m-10) REVERT: A 437 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.4678 (mpt-90) REVERT: A 478 ARG cc_start: 0.5478 (OUTLIER) cc_final: 0.5276 (ttp80) REVERT: A 561 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: A 699 ASP cc_start: 0.8466 (t0) cc_final: 0.8169 (t0) REVERT: A 841 GLN cc_start: 0.8518 (tt0) cc_final: 0.8265 (tt0) REVERT: A 864 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8166 (ttm-80) REVERT: A 882 HIS cc_start: 0.8381 (m-70) cc_final: 0.6545 (p90) REVERT: A 908 LYS cc_start: 0.8427 (mmtm) cc_final: 0.8097 (mmmt) REVERT: B 54 ASP cc_start: 0.7943 (m-30) cc_final: 0.7612 (m-30) outliers start: 26 outliers final: 13 residues processed: 98 average time/residue: 1.2557 time to fit residues: 130.3690 Evaluate side-chains 95 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 793 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7907 Z= 0.168 Angle : 0.529 7.089 10768 Z= 0.259 Chirality : 0.043 0.151 1143 Planarity : 0.004 0.039 1412 Dihedral : 4.765 38.764 1132 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.05 % Allowed : 18.31 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.48 (0.28), residues: 944 helix: 2.02 (0.44), residues: 154 sheet: 0.26 (0.35), residues: 238 loop : -1.33 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 501 HIS 0.005 0.001 HIS A 678 PHE 0.012 0.001 PHE A 101 TYR 0.007 0.001 TYR A 477 ARG 0.002 0.000 ARG A 864 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.938 Fit side-chains REVERT: A 107 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7663 (mt-10) REVERT: A 228 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6441 (mp0) REVERT: A 416 PHE cc_start: 0.7464 (m-80) cc_final: 0.7171 (m-10) REVERT: A 561 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: A 699 ASP cc_start: 0.8466 (t0) cc_final: 0.8173 (t0) REVERT: A 841 GLN cc_start: 0.8513 (tt0) cc_final: 0.8262 (tt0) REVERT: A 864 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.8161 (ttm-80) REVERT: A 908 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8119 (mmmt) REVERT: B 54 ASP cc_start: 0.7895 (m-30) cc_final: 0.7552 (m-30) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 1.2498 time to fit residues: 126.0282 Evaluate side-chains 94 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 744 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 HIS A 732 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7907 Z= 0.323 Angle : 0.611 6.989 10768 Z= 0.304 Chirality : 0.046 0.160 1143 Planarity : 0.005 0.038 1412 Dihedral : 5.131 43.213 1132 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.53 % Allowed : 18.31 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.72 (0.27), residues: 944 helix: 1.73 (0.44), residues: 154 sheet: 0.00 (0.34), residues: 241 loop : -1.41 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 540 HIS 0.005 0.001 HIS A 678 PHE 0.014 0.001 PHE B 48 TYR 0.015 0.001 TYR A 498 ARG 0.006 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.813 Fit side-chains REVERT: A 228 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6594 (mp0) REVERT: A 253 MET cc_start: 0.8151 (mmt) cc_final: 0.7924 (mmm) REVERT: A 416 PHE cc_start: 0.7593 (m-80) cc_final: 0.7214 (m-10) REVERT: A 437 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.4699 (mpt-90) REVERT: A 561 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: A 699 ASP cc_start: 0.8478 (t0) cc_final: 0.8193 (t0) REVERT: A 750 ASP cc_start: 0.8493 (p0) cc_final: 0.8197 (p0) REVERT: A 841 GLN cc_start: 0.8521 (tt0) cc_final: 0.8248 (tt0) REVERT: A 908 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8078 (mmmt) REVERT: A 918 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: B 54 ASP cc_start: 0.7936 (m-30) cc_final: 0.7578 (m-30) outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 1.2973 time to fit residues: 128.0401 Evaluate side-chains 91 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 918 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 HIS A 732 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7907 Z= 0.261 Angle : 0.586 7.775 10768 Z= 0.289 Chirality : 0.045 0.156 1143 Planarity : 0.004 0.038 1412 Dihedral : 5.061 43.133 1132 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.05 % Allowed : 19.40 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.71 (0.27), residues: 944 helix: 1.73 (0.44), residues: 152 sheet: 0.08 (0.35), residues: 235 loop : -1.42 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 540 HIS 0.007 0.001 HIS A 678 PHE 0.012 0.001 PHE B 48 TYR 0.009 0.001 TYR A 477 ARG 0.007 0.000 ARG A 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.886 Fit side-chains REVERT: A 107 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7798 (mt-10) REVERT: A 228 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6569 (mp0) REVERT: A 416 PHE cc_start: 0.7573 (m-80) cc_final: 0.7233 (m-10) REVERT: A 437 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.4601 (mpt-90) REVERT: A 561 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: A 699 ASP cc_start: 0.8467 (t0) cc_final: 0.8177 (t0) REVERT: A 841 GLN cc_start: 0.8516 (tt0) cc_final: 0.8213 (tt0) REVERT: A 864 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8139 (ttm-80) REVERT: A 908 LYS cc_start: 0.8437 (mmtm) cc_final: 0.8063 (mmmt) REVERT: B 54 ASP cc_start: 0.7875 (m-30) cc_final: 0.7535 (m-30) outliers start: 17 outliers final: 13 residues processed: 88 average time/residue: 1.2582 time to fit residues: 117.4791 Evaluate side-chains 91 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 798 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.0000 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 HIS ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109993 restraints weight = 12806.827| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.28 r_work: 0.3300 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7907 Z= 0.190 Angle : 0.554 8.258 10768 Z= 0.271 Chirality : 0.043 0.152 1143 Planarity : 0.004 0.039 1412 Dihedral : 4.822 40.891 1132 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.69 % Allowed : 19.76 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.56 (0.28), residues: 944 helix: 1.85 (0.44), residues: 152 sheet: 0.22 (0.35), residues: 237 loop : -1.35 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 501 HIS 0.009 0.001 HIS A 678 PHE 0.011 0.001 PHE A 101 TYR 0.010 0.001 TYR A 477 ARG 0.007 0.000 ARG A 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.47 seconds wall clock time: 52 minutes 39.60 seconds (3159.60 seconds total)