Starting phenix.real_space_refine on Thu Feb 15 11:32:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkp_12213/02_2024/7bkp_12213_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkp_12213/02_2024/7bkp_12213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkp_12213/02_2024/7bkp_12213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkp_12213/02_2024/7bkp_12213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkp_12213/02_2024/7bkp_12213_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkp_12213/02_2024/7bkp_12213_trim_updated.pdb" } resolution = 2.8 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= 0.002 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 31 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 3779 2.51 5 N 1073 2.21 5 O 1243 1.98 5 H 5956 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 806": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 896": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 12118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 11183 Classifications: {'peptide': 689} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Z" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 439 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 11} Link IDs: {'rna3p': 13} Chain: "X" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 463 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9390 SG CYS A 907 78.511 39.319 39.138 1.00 41.60 S ATOM 9436 SG CYS A 910 81.648 40.313 39.827 1.00 44.18 S ATOM 10206 SG CYS A 962 80.682 39.924 43.276 1.00 44.38 S ATOM 10238 SG CYS A 964 80.394 41.880 40.841 1.00 45.58 S Time building chain proxies: 10.41, per 1000 atoms: 0.86 Number of scatterers: 12118 At special positions: 0 Unit cell: (103.2, 89.44, 71.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 34 16.00 P 31 15.00 Mg 1 11.99 O 1243 8.00 N 1073 7.00 C 3779 6.00 H 5956 1.00 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: 9.91 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " Number of angles added : 6 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 5 sheets defined 47.8% alpha, 10.6% beta 14 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 7.05 Creating SS restraints... Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.928A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 336 through 353 Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 401 through 407 Processing helix chain 'A' and resid 415 through 427 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 454 through 474 removed outlier: 4.176A pdb=" N LYS A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 549 through 565 Processing helix chain 'A' and resid 577 through 593 Processing helix chain 'A' and resid 599 through 617 removed outlier: 3.531A pdb=" N THR A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 642 removed outlier: 3.668A pdb=" N PHE A 630 " --> pdb=" O HIS A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 699 through 713 Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.647A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 890 removed outlier: 3.924A pdb=" N ARG A 890 " --> pdb=" O MET A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 945 through 948 No H-bonds generated for 'chain 'A' and resid 945 through 948' Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing sheet with id= A, first strand: chain 'A' and resid 326 through 329 Processing sheet with id= B, first strand: chain 'A' and resid 537 through 543 Processing sheet with id= C, first strand: chain 'A' and resid 987 through 990 removed outlier: 3.710A pdb=" N CYS A 915 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 921 through 923 Processing sheet with id= E, first strand: chain 'A' and resid 977 through 982 removed outlier: 6.762A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 10.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5946 1.04 - 1.24: 618 1.24 - 1.44: 2066 1.44 - 1.63: 3589 1.63 - 1.83: 54 Bond restraints: 12273 Sorted by residual: bond pdb=" C4 ATP A1102 " pdb=" C5 ATP A1102 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 bond pdb=" C5 ATP A1102 " pdb=" C6 ATP A1102 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.05e+01 bond pdb=" C5 ATP A1102 " pdb=" N7 ATP A1102 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.42e+01 bond pdb=" C4 ATP A1102 " pdb=" N9 ATP A1102 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.22e+01 bond pdb=" C8 ATP A1102 " pdb=" N7 ATP A1102 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.90e+01 ... (remaining 12268 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.88: 223 104.88 - 112.62: 14476 112.62 - 120.36: 4131 120.36 - 128.10: 3355 128.10 - 135.84: 73 Bond angle restraints: 22258 Sorted by residual: angle pdb=" PB ATP A1102 " pdb=" O3B ATP A1102 " pdb=" PG ATP A1102 " ideal model delta sigma weight residual 139.87 117.82 22.05 1.00e+00 1.00e+00 4.86e+02 angle pdb=" PA ATP A1102 " pdb=" O3A ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 136.83 117.22 19.61 1.00e+00 1.00e+00 3.85e+02 angle pdb=" C5 ATP A1102 " pdb=" C4 ATP A1102 " pdb=" N3 ATP A1102 " ideal model delta sigma weight residual 126.80 118.91 7.89 1.00e+00 1.00e+00 6.22e+01 angle pdb=" N3 ATP A1102 " pdb=" C4 ATP A1102 " pdb=" N9 ATP A1102 " ideal model delta sigma weight residual 127.04 135.16 -8.12 1.15e+00 7.59e-01 5.00e+01 angle pdb=" N1 ATP A1102 " pdb=" C2 ATP A1102 " pdb=" N3 ATP A1102 " ideal model delta sigma weight residual 128.69 123.57 5.12 1.00e+00 1.00e+00 2.62e+01 ... (remaining 22253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 5543 35.84 - 71.67: 196 71.67 - 107.51: 14 107.51 - 143.35: 0 143.35 - 179.18: 9 Dihedral angle restraints: 5762 sinusoidal: 3461 harmonic: 2301 Sorted by residual: dihedral pdb=" CA SER A 995 " pdb=" C SER A 995 " pdb=" N PRO A 996 " pdb=" CA PRO A 996 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ASN A 549 " pdb=" C ASN A 549 " pdb=" N PRO A 550 " pdb=" CA PRO A 550 " ideal model delta harmonic sigma weight residual -180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C LYS A 451 " pdb=" N LYS A 451 " pdb=" CA LYS A 451 " pdb=" CB LYS A 451 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 5759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 816 0.066 - 0.133: 172 0.133 - 0.199: 6 0.199 - 0.265: 0 0.265 - 0.332: 1 Chirality restraints: 995 Sorted by residual: chirality pdb=" CA LYS A 451 " pdb=" N LYS A 451 " pdb=" C LYS A 451 " pdb=" CB LYS A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C2' ATP A1102 " pdb=" C1' ATP A1102 " pdb=" C3' ATP A1102 " pdb=" O2' ATP A1102 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" C4' C Z 11 " pdb=" C5' C Z 11 " pdb=" O4' C Z 11 " pdb=" C3' C Z 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.34 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 992 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 450 " 0.206 2.00e-02 2.50e+03 2.43e-01 8.87e+02 pdb=" CG ASN A 450 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 450 " -0.197 2.00e-02 2.50e+03 pdb=" ND2 ASN A 450 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 450 " 0.373 2.00e-02 2.50e+03 pdb="HD22 ASN A 450 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 890 " -0.020 9.50e-02 1.11e+02 2.06e-02 8.65e+00 pdb=" NE ARG A 890 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 890 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 890 " -0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 890 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A 890 " 0.021 2.00e-02 2.50e+03 pdb="HH12 ARG A 890 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG A 890 " 0.023 2.00e-02 2.50e+03 pdb="HH22 ARG A 890 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 995 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 996 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 996 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 996 " -0.021 5.00e-02 4.00e+02 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 539 2.18 - 2.79: 23958 2.79 - 3.39: 29686 3.39 - 4.00: 40619 4.00 - 4.60: 64350 Nonbonded interactions: 159152 Sorted by model distance: nonbonded pdb=" OE1 GLU A 671 " pdb=" H GLU A 671 " model vdw 1.577 1.850 nonbonded pdb=" HE2 HIS A 347 " pdb=" OG SER A 439 " model vdw 1.627 1.850 nonbonded pdb=" OE1 GLU A 842 " pdb=" H GLU A 842 " model vdw 1.645 1.850 nonbonded pdb=" HG1 THR A 727 " pdb=" OG SER A 730 " model vdw 1.684 1.850 nonbonded pdb=" O LYS A 750 " pdb=" H ASN A 784 " model vdw 1.699 1.850 ... (remaining 159147 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: 1.010 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: 0.190 Extract box with map and model: 5.210 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 55.170 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.009 0.080 6317 Z= 0.611 Angle : 0.836 22.048 8635 Z= 0.555 Chirality : 0.049 0.332 995 Planarity : 0.004 0.038 991 Dihedral : 15.132 82.134 2655 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.46 % Favored : 93.25 % Rotamer: Outliers : 0.32 % Allowed : 4.21 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.29), residues: 681 helix: -0.48 (0.25), residues: 353 sheet: -1.22 (0.48), residues: 103 loop : -2.94 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 737 HIS 0.004 0.001 HIS A 753 PHE 0.012 0.001 PHE A 675 TYR 0.013 0.001 TYR A 381 ARG 0.008 0.001 ARG A 890 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.041 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 3.3495 time to fit residues: 357.9035 Evaluate side-chains 44 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6317 Z= 0.147 Angle : 0.515 5.371 8635 Z= 0.274 Chirality : 0.038 0.152 995 Planarity : 0.004 0.049 991 Dihedral : 14.608 73.656 1210 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.85 % Favored : 95.01 % Rotamer: Outliers : 1.30 % Allowed : 11.35 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.25 (0.33), residues: 681 helix: 1.41 (0.28), residues: 347 sheet: -0.71 (0.50), residues: 103 loop : -2.43 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.003 0.001 HIS A 604 PHE 0.010 0.001 PHE A 680 TYR 0.010 0.001 TYR A 830 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 1.020 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 2.3261 time to fit residues: 113.5834 Evaluate side-chains 39 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 902 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6317 Z= 0.140 Angle : 0.462 4.437 8635 Z= 0.250 Chirality : 0.038 0.142 995 Planarity : 0.003 0.037 991 Dihedral : 14.099 73.870 1209 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.70 % Favored : 95.15 % Rotamer: Outliers : 1.13 % Allowed : 11.02 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.35), residues: 681 helix: 2.29 (0.29), residues: 346 sheet: -0.41 (0.49), residues: 103 loop : -2.08 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 737 HIS 0.002 0.001 HIS A 604 PHE 0.011 0.001 PHE A 680 TYR 0.009 0.001 TYR A 631 ARG 0.002 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 1.009 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 2.4499 time to fit residues: 114.1619 Evaluate side-chains 40 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 902 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.0870 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6317 Z= 0.162 Angle : 0.479 4.347 8635 Z= 0.260 Chirality : 0.038 0.138 995 Planarity : 0.003 0.034 991 Dihedral : 13.994 73.641 1209 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 1.30 % Allowed : 11.51 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.95 (0.34), residues: 681 helix: 2.58 (0.29), residues: 339 sheet: -0.26 (0.50), residues: 103 loop : -1.97 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 737 HIS 0.002 0.001 HIS A 921 PHE 0.008 0.001 PHE A 680 TYR 0.011 0.001 TYR A 312 ARG 0.002 0.000 ARG A 860 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 822 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7396 (mmt90) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 2.6665 time to fit residues: 123.9391 Evaluate side-chains 39 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 902 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6317 Z= 0.276 Angle : 0.564 5.909 8635 Z= 0.310 Chirality : 0.041 0.144 995 Planarity : 0.004 0.041 991 Dihedral : 14.189 73.550 1209 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 1.94 % Allowed : 11.51 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.68 (0.34), residues: 681 helix: 2.27 (0.28), residues: 338 sheet: -0.09 (0.51), residues: 103 loop : -2.10 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 737 HIS 0.004 0.001 HIS A 921 PHE 0.011 0.001 PHE A 374 TYR 0.014 0.002 TYR A 312 ARG 0.003 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.932 Fit side-chains REVERT: A 822 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7558 (mmt90) outliers start: 12 outliers final: 6 residues processed: 46 average time/residue: 2.8775 time to fit residues: 139.0072 Evaluate side-chains 41 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1012 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 0.0050 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6317 Z= 0.232 Angle : 0.536 5.637 8635 Z= 0.294 Chirality : 0.040 0.141 995 Planarity : 0.004 0.038 991 Dihedral : 14.174 73.903 1209 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.94 % Allowed : 12.16 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.34), residues: 681 helix: 2.34 (0.28), residues: 338 sheet: -0.12 (0.50), residues: 103 loop : -2.08 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 737 HIS 0.003 0.001 HIS A 447 PHE 0.011 0.001 PHE A 374 TYR 0.011 0.001 TYR A 312 ARG 0.002 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 822 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7656 (mmt90) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 2.6302 time to fit residues: 130.3595 Evaluate side-chains 43 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1012 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6317 Z= 0.156 Angle : 0.477 5.503 8635 Z= 0.259 Chirality : 0.038 0.141 995 Planarity : 0.003 0.038 991 Dihedral : 14.050 73.711 1209 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.13 % Allowed : 12.80 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.35), residues: 681 helix: 2.58 (0.29), residues: 343 sheet: -0.20 (0.50), residues: 103 loop : -1.77 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 753 PHE 0.010 0.001 PHE A 680 TYR 0.010 0.001 TYR A1000 ARG 0.001 0.000 ARG A 779 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 822 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7722 (mmt90) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 2.6487 time to fit residues: 120.2254 Evaluate side-chains 41 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6317 Z= 0.209 Angle : 0.509 5.666 8635 Z= 0.278 Chirality : 0.039 0.139 995 Planarity : 0.003 0.037 991 Dihedral : 14.087 73.616 1209 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.58 % Favored : 94.27 % Rotamer: Outliers : 1.62 % Allowed : 12.97 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.34), residues: 681 helix: 2.50 (0.29), residues: 343 sheet: -0.17 (0.50), residues: 103 loop : -1.78 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 737 HIS 0.002 0.001 HIS A 447 PHE 0.009 0.001 PHE A 374 TYR 0.011 0.001 TYR A 312 ARG 0.003 0.000 ARG A 860 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 1.004 Fit side-chains REVERT: A 822 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7775 (mmt90) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 2.7305 time to fit residues: 129.4731 Evaluate side-chains 43 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1012 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6317 Z= 0.154 Angle : 0.474 5.080 8635 Z= 0.257 Chirality : 0.038 0.140 995 Planarity : 0.003 0.037 991 Dihedral : 14.026 73.723 1209 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.81 % Allowed : 13.61 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.35), residues: 681 helix: 2.72 (0.29), residues: 342 sheet: -0.20 (0.50), residues: 103 loop : -1.68 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 753 PHE 0.010 0.001 PHE A 680 TYR 0.009 0.001 TYR A1000 ARG 0.002 0.000 ARG A 860 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 822 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7763 (mmt90) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 2.6328 time to fit residues: 114.1118 Evaluate side-chains 40 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6317 Z= 0.152 Angle : 0.467 5.090 8635 Z= 0.253 Chirality : 0.038 0.138 995 Planarity : 0.003 0.036 991 Dihedral : 13.992 73.702 1209 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.81 % Allowed : 13.61 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.35), residues: 681 helix: 2.80 (0.29), residues: 342 sheet: -0.17 (0.50), residues: 103 loop : -1.65 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 347 PHE 0.009 0.001 PHE A 680 TYR 0.009 0.001 TYR A 312 ARG 0.002 0.000 ARG A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 822 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7771 (mmt90) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 2.5671 time to fit residues: 111.1737 Evaluate side-chains 40 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087739 restraints weight = 19909.983| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.83 r_work: 0.2967 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6317 Z= 0.128 Angle : 0.450 5.203 8635 Z= 0.242 Chirality : 0.037 0.142 995 Planarity : 0.003 0.035 991 Dihedral : 13.932 73.652 1209 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.65 % Allowed : 13.78 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.35), residues: 681 helix: 2.93 (0.29), residues: 342 sheet: -0.14 (0.51), residues: 103 loop : -1.54 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 737 HIS 0.002 0.001 HIS A 753 PHE 0.009 0.001 PHE A 680 TYR 0.009 0.001 TYR A1000 ARG 0.002 0.000 ARG A 860 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4375.46 seconds wall clock time: 77 minutes 35.82 seconds (4655.82 seconds total)