Starting phenix.real_space_refine on Tue Apr 9 06:10:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/04_2024/8pjb_17703_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/04_2024/8pjb_17703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/04_2024/8pjb_17703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/04_2024/8pjb_17703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/04_2024/8pjb_17703_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/04_2024/8pjb_17703_updated.pdb" } resolution = 3.62 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7765 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 4933 2.51 5 N 1357 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A ARG 905": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7840 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7632 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 962, 7621 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 915} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 962, 7621 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 915} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7754 Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.18, per 1000 atoms: 1.04 Number of scatterers: 7840 At special positions: 0 Unit cell: (87.132, 96.174, 104.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 11 15.00 Mg 1 11.99 O 1490 8.00 N 1357 7.00 C 4933 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: 3.09 Conformation dependent library (CDL) restraints added in 3.2 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 7 sheets defined 44.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 167 through 180 removed outlier: 4.085A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.937A pdb=" N LYS A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.861A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 4.281A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 487 through 496 removed outlier: 4.399A pdb=" N GLU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.742A pdb=" N VAL A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 830 through 843 Processing helix chain 'A' and resid 854 through 860 Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 881 through 891 Processing helix chain 'A' and resid 911 through 914 No H-bonds generated for 'chain 'A' and resid 911 through 914' Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 921 through 938 removed outlier: 3.505A pdb=" N ARG A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 950 Processing helix chain 'A' and resid 954 through 974 Processing helix chain 'A' and resid 978 through 981 Processing helix chain 'A' and resid 995 through 1007 removed outlier: 3.822A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1077 Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1102 through 1124 removed outlier: 4.065A pdb=" N LEU A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) Proline residue: A1113 - end of helix Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1134 through 1146 Processing sheet with id= A, first strand: chain 'A' and resid 200 through 202 removed outlier: 3.545A pdb=" N PHE A 200 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 221 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 555 through 559 removed outlier: 6.695A pdb=" N VAL A 535 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE A 405 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 537 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY A 407 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 539 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 481 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL A 438 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 483 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLN A 440 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS A 485 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR A 486 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 567 through 569 removed outlier: 7.095A pdb=" N ALA A 655 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL A 732 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 657 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP A 734 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE A 659 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 737 through 744 Processing sheet with id= E, first strand: chain 'A' and resid 1049 through 1051 removed outlier: 6.949A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1054 through 1056 Processing sheet with id= G, first strand: chain 'A' and resid 1082 through 1084 311 hydrogen bonds defined for protein. 900 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: 2.54 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1295 1.30 - 1.43: 1991 1.43 - 1.56: 4627 1.56 - 1.69: 20 1.69 - 1.81: 73 Bond restraints: 8006 Sorted by residual: bond pdb=" CA SER A 222 " pdb=" CB SER A 222 " ideal model delta sigma weight residual 1.533 1.458 0.075 1.60e-02 3.91e+03 2.17e+01 bond pdb=" CA SER A 892 " pdb=" CB SER A 892 " ideal model delta sigma weight residual 1.530 1.453 0.077 1.69e-02 3.50e+03 2.08e+01 bond pdb=" C PRO A 191 " pdb=" O PRO A 191 " ideal model delta sigma weight residual 1.233 1.177 0.056 1.24e-02 6.50e+03 2.06e+01 bond pdb=" CA ALA A 202 " pdb=" CB ALA A 202 " ideal model delta sigma weight residual 1.533 1.455 0.078 1.72e-02 3.38e+03 2.03e+01 bond pdb=" CA SER A 891 " pdb=" CB SER A 891 " ideal model delta sigma weight residual 1.528 1.469 0.058 1.35e-02 5.49e+03 1.85e+01 ... (remaining 8001 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.89: 148 103.89 - 111.96: 3933 111.96 - 120.03: 3401 120.03 - 128.10: 3350 128.10 - 136.16: 49 Bond angle restraints: 10881 Sorted by residual: angle pdb=" C3' U C 9 " pdb=" O3' U C 9 " pdb=" P U C 10 " ideal model delta sigma weight residual 120.20 103.40 16.80 1.50e+00 4.44e-01 1.25e+02 angle pdb=" C3' U C 3 " pdb=" O3' U C 3 " pdb=" P C C 4 " ideal model delta sigma weight residual 120.20 107.33 12.87 1.50e+00 4.44e-01 7.36e+01 angle pdb=" C3' C C 2 " pdb=" O3' C C 2 " pdb=" P U C 3 " ideal model delta sigma weight residual 120.20 108.63 11.57 1.50e+00 4.44e-01 5.95e+01 angle pdb=" N ARG A1059 " pdb=" CA ARG A1059 " pdb=" C ARG A1059 " ideal model delta sigma weight residual 112.72 104.35 8.37 1.14e+00 7.69e-01 5.39e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N SER A 222 " ideal model delta sigma weight residual 114.58 120.82 -6.24 8.60e-01 1.35e+00 5.26e+01 ... (remaining 10876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.73: 4197 18.73 - 37.45: 521 37.45 - 56.18: 163 56.18 - 74.91: 48 74.91 - 93.63: 8 Dihedral angle restraints: 4937 sinusoidal: 2111 harmonic: 2826 Sorted by residual: dihedral pdb=" CD ARG A 905 " pdb=" NE ARG A 905 " pdb=" CZ ARG A 905 " pdb=" NH1 ARG A 905 " ideal model delta sinusoidal sigma weight residual 0.00 -77.76 77.76 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CD ARG A 590 " pdb=" NE ARG A 590 " pdb=" CZ ARG A 590 " pdb=" NH1 ARG A 590 " ideal model delta sinusoidal sigma weight residual 0.00 -64.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " pdb=" CZ ARG A 198 " pdb=" NH1 ARG A 198 " ideal model delta sinusoidal sigma weight residual 0.00 -53.38 53.38 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 4934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1171 0.112 - 0.224: 64 0.224 - 0.336: 11 0.336 - 0.448: 4 0.448 - 0.561: 1 Chirality restraints: 1251 Sorted by residual: chirality pdb=" P C C 2 " pdb=" OP1 C C 2 " pdb=" OP2 C C 2 " pdb=" O5' C C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" P C C 4 " pdb=" OP1 C C 4 " pdb=" OP2 C C 4 " pdb=" O5' C C 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" P U C 3 " pdb=" OP1 U C 3 " pdb=" OP2 U C 3 " pdb=" O5' U C 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 1248 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 905 " 1.064 9.50e-02 1.11e+02 4.77e-01 1.37e+02 pdb=" NE ARG A 905 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 905 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 905 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 905 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 590 " -0.989 9.50e-02 1.11e+02 4.43e-01 1.19e+02 pdb=" NE ARG A 590 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 590 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 590 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 590 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 198 " -0.881 9.50e-02 1.11e+02 3.95e-01 9.45e+01 pdb=" NE ARG A 198 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 198 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 198 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 198 " -0.024 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 168 2.66 - 3.22: 7403 3.22 - 3.78: 12296 3.78 - 4.34: 16242 4.34 - 4.90: 26454 Nonbonded interactions: 62563 Sorted by model distance: nonbonded pdb=" OG1 THR A 414 " pdb=" OD2 ASP A 507 " model vdw 2.096 2.440 nonbonded pdb=" OE1 GLN A 621 " pdb=" NH2 ARG A 624 " model vdw 2.266 2.520 nonbonded pdb=" O GLN A 332 " pdb=" OH TYR A 479 " model vdw 2.282 2.440 nonbonded pdb=" OE1 GLN A 440 " pdb=" OG SER A 445 " model vdw 2.296 2.440 nonbonded pdb=" OG ASER A1070 " pdb=" NE2 GLN A1073 " model vdw 2.316 2.520 ... (remaining 62558 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 3.830 Check model and map are aligned: 0.130 Set scattering table: 0.060 Process input model: 31.390 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.006 0.078 8006 Z= 0.363 Angle : 0.985 16.796 10881 Z= 0.618 Chirality : 0.063 0.561 1251 Planarity : 0.026 0.477 1371 Dihedral : 18.757 93.633 3097 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 1.15 % Allowed : 5.65 % Favored : 93.20 % Rotamer: Outliers : 4.25 % Allowed : 22.67 % Favored : 73.08 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 2.13 % 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: -0.17 (0.28), residues: 958 helix: 1.03 (0.25), residues: 443 sheet: -0.98 (0.43), residues: 148 loop : -1.08 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.007 0.001 HIS A 910 PHE 0.029 0.002 PHE A 240 TYR 0.015 0.002 TYR A 550 ARG 0.008 0.001 ARG A 867 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 10 residues processed: 194 average time/residue: 0.2147 time to fit residues: 55.7108 Evaluate side-chains 123 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1057 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 0.2980 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8006 Z= 0.195 Angle : 0.752 14.123 10881 Z= 0.356 Chirality : 0.043 0.253 1251 Planarity : 0.006 0.135 1371 Dihedral : 10.106 79.603 1225 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.02 % Favored : 94.56 % Rotamer: Outliers : 3.54 % Allowed : 27.04 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.05 (0.27), residues: 958 helix: 0.95 (0.24), residues: 452 sheet: -0.67 (0.45), residues: 139 loop : -0.72 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 328 HIS 0.006 0.002 HIS A 503 PHE 0.034 0.001 PHE A 155 TYR 0.021 0.002 TYR A 420 ARG 0.009 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 253 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7803 (mmmt) outliers start: 29 outliers final: 19 residues processed: 147 average time/residue: 0.1903 time to fit residues: 39.0355 Evaluate side-chains 133 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 664 ASN ** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8006 Z= 0.191 Angle : 0.725 11.677 10881 Z= 0.340 Chirality : 0.042 0.215 1251 Planarity : 0.005 0.114 1371 Dihedral : 9.610 78.343 1211 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.29 % Favored : 95.40 % Rotamer: Outliers : 3.78 % Allowed : 25.74 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.15 (0.28), residues: 958 helix: 1.06 (0.25), residues: 451 sheet: -0.41 (0.44), residues: 145 loop : -0.81 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 328 HIS 0.007 0.001 HIS A 646 PHE 0.023 0.001 PHE A 155 TYR 0.032 0.002 TYR A 420 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 MET cc_start: 0.6294 (ptm) cc_final: 0.6014 (ptm) outliers start: 31 outliers final: 20 residues processed: 144 average time/residue: 0.1724 time to fit residues: 35.6216 Evaluate side-chains 133 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN ** A1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8006 Z= 0.224 Angle : 0.707 12.394 10881 Z= 0.335 Chirality : 0.043 0.208 1251 Planarity : 0.005 0.104 1371 Dihedral : 9.337 78.624 1207 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.50 % Favored : 95.19 % Rotamer: Outliers : 4.13 % Allowed : 25.27 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.23 (0.28), residues: 958 helix: 1.18 (0.25), residues: 450 sheet: -0.44 (0.44), residues: 145 loop : -0.83 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 328 HIS 0.009 0.001 HIS A1032 PHE 0.016 0.001 PHE A1045 TYR 0.028 0.002 TYR A 420 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 MET cc_start: 0.6320 (ptm) cc_final: 0.6019 (ptm) outliers start: 34 outliers final: 24 residues processed: 135 average time/residue: 0.1723 time to fit residues: 33.8584 Evaluate side-chains 132 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 0.0670 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN ** A1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8006 Z= 0.282 Angle : 0.723 10.614 10881 Z= 0.346 Chirality : 0.043 0.202 1251 Planarity : 0.005 0.099 1371 Dihedral : 9.328 78.932 1206 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 4.13 % Allowed : 25.62 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.20 (0.28), residues: 958 helix: 1.16 (0.25), residues: 451 sheet: -0.51 (0.45), residues: 147 loop : -0.82 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 328 HIS 0.006 0.001 HIS A 503 PHE 0.017 0.001 PHE A1045 TYR 0.010 0.001 TYR A 420 ARG 0.004 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 28 residues processed: 124 average time/residue: 0.1670 time to fit residues: 30.1514 Evaluate side-chains 129 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1094 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8006 Z= 0.326 Angle : 0.758 12.940 10881 Z= 0.364 Chirality : 0.044 0.202 1251 Planarity : 0.005 0.098 1371 Dihedral : 9.294 78.813 1204 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 4.49 % Allowed : 25.50 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.12 (0.28), residues: 958 helix: 1.16 (0.25), residues: 447 sheet: -0.67 (0.46), residues: 150 loop : -0.87 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 328 HIS 0.008 0.002 HIS A 910 PHE 0.014 0.001 PHE A 484 TYR 0.012 0.002 TYR A 420 ARG 0.005 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 31 residues processed: 119 average time/residue: 0.1727 time to fit residues: 29.4836 Evaluate side-chains 126 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1094 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 55 optimal weight: 6.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A 958 ASN ** A1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8006 Z= 0.192 Angle : 0.720 12.327 10881 Z= 0.339 Chirality : 0.044 0.202 1251 Planarity : 0.005 0.096 1371 Dihedral : 9.154 76.205 1204 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.50 % Favored : 95.29 % Rotamer: Outliers : 4.25 % Allowed : 26.80 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 958 helix: 1.22 (0.25), residues: 444 sheet: -0.69 (0.45), residues: 152 loop : -0.73 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 328 HIS 0.005 0.001 HIS A 910 PHE 0.008 0.001 PHE A 580 TYR 0.008 0.001 TYR A 752 ARG 0.004 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7515 (p) outliers start: 35 outliers final: 29 residues processed: 128 average time/residue: 0.1789 time to fit residues: 32.4836 Evaluate side-chains 130 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1094 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A1065 GLN A1094 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8006 Z= 0.253 Angle : 0.748 11.168 10881 Z= 0.356 Chirality : 0.044 0.201 1251 Planarity : 0.005 0.095 1371 Dihedral : 9.201 76.521 1204 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 4.25 % Allowed : 26.92 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.24 (0.28), residues: 958 helix: 1.28 (0.25), residues: 443 sheet: -0.72 (0.44), residues: 152 loop : -0.77 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP A 328 HIS 0.006 0.001 HIS A 910 PHE 0.013 0.001 PHE A1045 TYR 0.009 0.001 TYR A 420 ARG 0.004 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7559 (p) outliers start: 35 outliers final: 29 residues processed: 117 average time/residue: 0.2234 time to fit residues: 36.7532 Evaluate side-chains 125 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1094 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A 746 HIS A 966 GLN A1094 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8006 Z= 0.192 Angle : 0.727 11.702 10881 Z= 0.343 Chirality : 0.043 0.203 1251 Planarity : 0.005 0.094 1371 Dihedral : 9.131 75.234 1204 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.50 % Favored : 95.29 % Rotamer: Outliers : 3.31 % Allowed : 27.63 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.24 (0.27), residues: 958 helix: 1.30 (0.25), residues: 442 sheet: -0.75 (0.45), residues: 142 loop : -0.78 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 328 HIS 0.004 0.001 HIS A 241 PHE 0.008 0.001 PHE A 798 TYR 0.009 0.001 TYR A 420 ARG 0.004 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 25 residues processed: 115 average time/residue: 0.1979 time to fit residues: 31.7086 Evaluate side-chains 116 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1094 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A 910 HIS A1094 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8006 Z= 0.197 Angle : 0.755 11.962 10881 Z= 0.352 Chirality : 0.043 0.202 1251 Planarity : 0.005 0.094 1371 Dihedral : 8.999 73.582 1200 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 3.42 % Allowed : 27.98 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 958 helix: 1.31 (0.25), residues: 442 sheet: -0.65 (0.45), residues: 142 loop : -0.77 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 328 HIS 0.006 0.001 HIS A 910 PHE 0.012 0.001 PHE A1045 TYR 0.016 0.001 TYR A1009 ARG 0.006 0.000 ARG A 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 26 residues processed: 114 average time/residue: 0.1812 time to fit residues: 29.3914 Evaluate side-chains 121 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1094 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.0970 chunk 70 optimal weight: 0.0970 chunk 11 optimal weight: 0.0020 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 664 ASN A 910 HIS A 966 GLN A1094 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.073014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.057201 restraints weight = 60778.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060079 restraints weight = 24338.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.062124 restraints weight = 14168.716| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8006 Z= 0.178 Angle : 0.764 12.546 10881 Z= 0.357 Chirality : 0.044 0.205 1251 Planarity : 0.005 0.092 1371 Dihedral : 8.972 73.528 1200 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.39 % Favored : 95.40 % Rotamer: Outliers : 3.31 % Allowed : 28.10 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.34 (0.28), residues: 958 helix: 1.32 (0.25), residues: 439 sheet: -0.63 (0.45), residues: 144 loop : -0.65 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 328 HIS 0.006 0.001 HIS A 910 PHE 0.008 0.001 PHE A 894 TYR 0.015 0.001 TYR A1009 ARG 0.007 0.000 ARG A 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.88 seconds wall clock time: 35 minutes 7.25 seconds (2107.25 seconds total)