Starting phenix.real_space_refine on Sat Dec 9 08:04:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iby_35349/12_2023/8iby_35349.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iby_35349/12_2023/8iby_35349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iby_35349/12_2023/8iby_35349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iby_35349/12_2023/8iby_35349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iby_35349/12_2023/8iby_35349.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iby_35349/12_2023/8iby_35349.pdb" } resolution = 3.47 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= 0.010 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 198 5.49 5 S 32 5.16 5 C 5817 2.51 5 N 1973 2.21 5 O 2482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 331": "OE1" <-> "OE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 490": "OD1" <-> "OD2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 642": "OE1" <-> "OE2" Residue "C TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 974": "OE1" <-> "OE2" Residue "C GLU 1021": "OE1" <-> "OE2" Residue "C GLU 1025": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10503 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 4233 Classifications: {'RNA': 198} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 17, 'rna3p_pur': 91, 'rna3p_pyr': 75} Link IDs: {'rna2p': 32, 'rna3p': 165} Chain breaks: 3 Chain: "C" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6269 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 39, 'TRANS': 753} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9132 SG CYS C 934 59.637 71.301 25.232 1.00104.66 S ATOM 9158 SG CYS C 938 58.180 73.110 22.172 1.00109.37 S ATOM 9263 SG CYS C 951 55.829 71.305 24.654 1.00 93.60 S Time building chain proxies: 6.36, per 1000 atoms: 0.61 Number of scatterers: 10503 At special positions: 0 Unit cell: (107.594, 130.65, 119.671, 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) Zn 1 29.99 S 32 16.00 P 198 15.00 O 2482 8.00 N 1973 7.00 C 5817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 946 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 934 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 938 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 951 " Number of angles added : 3 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 54.6% alpha, 10.5% beta 57 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'C' and resid 305 through 324 Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.553A pdb=" N ALA C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 365 through 373 Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.928A pdb=" N LYS C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.937A pdb=" N VAL C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.577A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 519 Processing helix chain 'C' and resid 539 through 549 Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 607 removed outlier: 3.628A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.624A pdb=" N MET C 640 " --> pdb=" O SER C 636 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN C 641 " --> pdb=" O LYS C 637 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 642 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 643 " --> pdb=" O GLY C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.564A pdb=" N GLN C 750 " --> pdb=" O ILE C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 755 removed outlier: 3.884A pdb=" N LEU C 755 " --> pdb=" O GLY C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 779 removed outlier: 3.802A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 791 removed outlier: 4.177A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 816 removed outlier: 3.740A pdb=" N ILE C 807 " --> pdb=" O VAL C 803 " (cutoff:3.500A) Proline residue: C 808 - end of helix Processing helix chain 'C' and resid 817 through 821 Processing helix chain 'C' and resid 823 through 831 removed outlier: 3.508A pdb=" N ARG C 827 " --> pdb=" O TRP C 823 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 831 " --> pdb=" O ARG C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 849 Processing helix chain 'C' and resid 861 through 871 Processing helix chain 'C' and resid 875 through 879 Processing helix chain 'C' and resid 884 through 889 removed outlier: 3.590A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 removed outlier: 3.679A pdb=" N VAL C 904 " --> pdb=" O GLY C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 922 removed outlier: 3.821A pdb=" N ARG C 922 " --> pdb=" O ARG C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 932 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 951 through 953 No H-bonds generated for 'chain 'C' and resid 951 through 953' Processing helix chain 'C' and resid 954 through 976 Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.736A pdb=" N LYS C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1045 Processing helix chain 'C' and resid 1066 through 1077 removed outlier: 3.710A pdb=" N ILE C1077 " --> pdb=" O LEU C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1105 removed outlier: 3.819A pdb=" N LEU C1084 " --> pdb=" O ARG C1080 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) Proline residue: C1088 - end of helix removed outlier: 4.317A pdb=" N MET C1105 " --> pdb=" O ARG C1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 467 Processing sheet with id=AA2, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.736A pdb=" N VAL C 631 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 528 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.736A pdb=" N VAL C 631 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 528 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 537 through 538 removed outlier: 4.429A pdb=" N VAL C 537 " --> pdb=" O GLY C 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 614 through 616 Processing sheet with id=AA6, first strand: chain 'C' and resid 686 through 687 Processing sheet with id=AA7, first strand: chain 'C' and resid 851 through 852 Processing sheet with id=AA8, first strand: chain 'C' and resid 979 through 982 removed outlier: 3.762A pdb=" N THR C 979 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C1000 " --> pdb=" O THR C 979 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY C1005 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR C1055 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C1064 " --> pdb=" O SER C1060 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 148 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2787 1.34 - 1.46: 3602 1.46 - 1.58: 4301 1.58 - 1.70: 394 1.70 - 1.83: 46 Bond restraints: 11130 Sorted by residual: bond pdb=" CB PRO C 366 " pdb=" CG PRO C 366 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.17e+00 bond pdb=" CB PRO C 915 " pdb=" CG PRO C 915 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.27e+00 bond pdb=" CG1 ILE C 959 " pdb=" CD1 ILE C 959 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CB GLU C 974 " pdb=" CG GLU C 974 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C PRO C 364 " pdb=" N THR C 365 " ideal model delta sigma weight residual 1.327 1.347 -0.020 1.71e-02 3.42e+03 1.40e+00 ... (remaining 11125 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.03: 987 105.03 - 112.29: 6036 112.29 - 119.55: 3781 119.55 - 126.81: 4614 126.81 - 134.07: 596 Bond angle restraints: 16014 Sorted by residual: angle pdb=" CA PRO C 366 " pdb=" N PRO C 366 " pdb=" CD PRO C 366 " ideal model delta sigma weight residual 112.00 104.01 7.99 1.40e+00 5.10e-01 3.26e+01 angle pdb=" CB MET C 428 " pdb=" CG MET C 428 " pdb=" SD MET C 428 " ideal model delta sigma weight residual 112.70 124.66 -11.96 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C3' C E 267 " pdb=" O3' C E 267 " pdb=" P C E 268 " ideal model delta sigma weight residual 120.20 125.96 -5.76 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C SER C 469 " pdb=" N ILE C 470 " pdb=" CA ILE C 470 " ideal model delta sigma weight residual 120.33 123.31 -2.98 8.00e-01 1.56e+00 1.39e+01 angle pdb=" CA PRO C 915 " pdb=" N PRO C 915 " pdb=" CD PRO C 915 " ideal model delta sigma weight residual 112.00 106.78 5.22 1.40e+00 5.10e-01 1.39e+01 ... (remaining 16009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 6167 35.45 - 70.90: 597 70.90 - 106.35: 71 106.35 - 141.80: 6 141.80 - 177.25: 3 Dihedral angle restraints: 6844 sinusoidal: 4570 harmonic: 2274 Sorted by residual: dihedral pdb=" O4' C E 145 " pdb=" C1' C E 145 " pdb=" N1 C E 145 " pdb=" C2 C E 145 " ideal model delta sinusoidal sigma weight residual -128.00 49.25 -177.25 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C4' U E 101 " pdb=" C3' U E 101 " pdb=" O3' U E 101 " pdb=" P G E 102 " ideal model delta sinusoidal sigma weight residual -140.00 29.63 -169.63 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" O4' G E 110 " pdb=" C1' G E 110 " pdb=" N9 G E 110 " pdb=" C4 G E 110 " ideal model delta sinusoidal sigma weight residual -106.00 -163.81 57.81 1 1.70e+01 3.46e-03 1.55e+01 ... (remaining 6841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1651 0.046 - 0.091: 225 0.091 - 0.137: 57 0.137 - 0.183: 6 0.183 - 0.229: 3 Chirality restraints: 1942 Sorted by residual: chirality pdb=" C1' A E 56 " pdb=" O4' A E 56 " pdb=" C2' A E 56 " pdb=" N9 A E 56 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" P C E 268 " pdb=" OP1 C E 268 " pdb=" OP2 C E 268 " pdb=" O5' C E 268 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' U E 114 " pdb=" C4' U E 114 " pdb=" O3' U E 114 " pdb=" C2' U E 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 1939 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 365 " -0.056 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 366 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 366 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 366 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C E 78 " 0.031 2.00e-02 2.50e+03 1.97e-02 8.77e+00 pdb=" N1 C E 78 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C E 78 " 0.023 2.00e-02 2.50e+03 pdb=" O2 C E 78 " -0.018 2.00e-02 2.50e+03 pdb=" N3 C E 78 " -0.011 2.00e-02 2.50e+03 pdb=" C4 C E 78 " 0.019 2.00e-02 2.50e+03 pdb=" N4 C E 78 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C E 78 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C E 78 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 914 " -0.047 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO C 915 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 915 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 915 " -0.038 5.00e-02 4.00e+02 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 909 2.73 - 3.27: 10255 3.27 - 3.81: 18936 3.81 - 4.36: 21763 4.36 - 4.90: 33231 Nonbonded interactions: 85094 Sorted by model distance: nonbonded pdb=" O2' G E 112 " pdb=" O4' A E 113 " model vdw 2.187 2.440 nonbonded pdb=" O LEU C 878 " pdb=" OG SER C 881 " model vdw 2.206 2.440 nonbonded pdb=" O2 U E 136 " pdb=" N2 G E 152 " model vdw 2.207 2.496 nonbonded pdb=" NZ LYS C 389 " pdb=" O PRO C 390 " model vdw 2.230 2.520 nonbonded pdb=" N2 G E 33 " pdb=" OP2 A E 36 " model vdw 2.233 2.520 ... (remaining 85089 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.540 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 39.160 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 11130 Z= 0.209 Angle : 0.622 11.963 16014 Z= 0.319 Chirality : 0.035 0.229 1942 Planarity : 0.005 0.081 1316 Dihedral : 23.001 177.250 5376 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 25.52 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.31), residues: 789 helix: 1.47 (0.28), residues: 371 sheet: -2.02 (0.62), residues: 63 loop : -1.11 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 388 HIS 0.010 0.001 HIS C 955 PHE 0.025 0.002 PHE C 555 TYR 0.015 0.001 TYR C 703 ARG 0.008 0.000 ARG C 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2904 time to fit residues: 30.5676 Evaluate side-chains 76 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 57 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 11130 Z= 0.143 Angle : 0.547 10.079 16014 Z= 0.273 Chirality : 0.034 0.223 1942 Planarity : 0.004 0.040 1316 Dihedral : 23.627 177.683 3837 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 1.64 % Allowed : 23.28 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.31), residues: 789 helix: 1.60 (0.28), residues: 386 sheet: -1.71 (0.63), residues: 64 loop : -1.06 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 388 HIS 0.007 0.001 HIS C 955 PHE 0.009 0.001 PHE C 749 TYR 0.011 0.001 TYR C1070 ARG 0.004 0.000 ARG C 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.895 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 89 average time/residue: 0.2823 time to fit residues: 35.1855 Evaluate side-chains 77 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1055 time to fit residues: 2.0121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.0370 chunk 89 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11130 Z= 0.206 Angle : 0.570 10.168 16014 Z= 0.285 Chirality : 0.035 0.216 1942 Planarity : 0.004 0.047 1316 Dihedral : 23.601 177.530 3837 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.68 % Rotamer: Outliers : 3.28 % Allowed : 23.13 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.31), residues: 789 helix: 1.48 (0.28), residues: 394 sheet: -2.00 (0.60), residues: 64 loop : -1.06 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 388 HIS 0.007 0.001 HIS C 955 PHE 0.007 0.001 PHE C 864 TYR 0.011 0.001 TYR C 563 ARG 0.004 0.000 ARG C 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.068 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 100 average time/residue: 0.2533 time to fit residues: 35.1617 Evaluate side-chains 79 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0965 time to fit residues: 2.5736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11130 Z= 0.162 Angle : 0.555 10.142 16014 Z= 0.274 Chirality : 0.035 0.218 1942 Planarity : 0.004 0.046 1316 Dihedral : 23.570 177.578 3837 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 1.64 % Allowed : 23.73 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.31), residues: 789 helix: 1.60 (0.28), residues: 389 sheet: -2.05 (0.60), residues: 64 loop : -1.00 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 388 HIS 0.008 0.001 HIS C 955 PHE 0.007 0.001 PHE C 749 TYR 0.007 0.001 TYR C 703 ARG 0.004 0.000 ARG C 611 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.926 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.2777 time to fit residues: 35.4414 Evaluate side-chains 74 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2484 time to fit residues: 3.7690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 80 optimal weight: 40.0000 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11130 Z= 0.391 Angle : 0.692 10.335 16014 Z= 0.346 Chirality : 0.040 0.242 1942 Planarity : 0.005 0.045 1316 Dihedral : 23.879 177.397 3837 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 2.24 % Allowed : 24.18 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.31), residues: 789 helix: 1.20 (0.27), residues: 387 sheet: -2.67 (0.53), residues: 69 loop : -1.18 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 388 HIS 0.011 0.002 HIS C 962 PHE 0.015 0.002 PHE C 597 TYR 0.012 0.002 TYR C 563 ARG 0.006 0.001 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.020 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 83 average time/residue: 0.2677 time to fit residues: 31.1133 Evaluate side-chains 80 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0987 time to fit residues: 3.0509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 55 optimal weight: 0.0670 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11130 Z= 0.192 Angle : 0.597 10.256 16014 Z= 0.294 Chirality : 0.036 0.259 1942 Planarity : 0.004 0.048 1316 Dihedral : 23.806 177.507 3837 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 1.19 % Allowed : 25.52 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.31), residues: 789 helix: 1.42 (0.28), residues: 389 sheet: -2.34 (0.56), residues: 64 loop : -1.13 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 388 HIS 0.006 0.001 HIS C 955 PHE 0.012 0.002 PHE C 429 TYR 0.007 0.001 TYR C1070 ARG 0.004 0.000 ARG C 987 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 80 average time/residue: 0.2892 time to fit residues: 32.1987 Evaluate side-chains 66 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1356 time to fit residues: 1.5997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11130 Z= 0.190 Angle : 0.605 11.566 16014 Z= 0.297 Chirality : 0.036 0.250 1942 Planarity : 0.004 0.050 1316 Dihedral : 23.784 177.571 3837 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 1.64 % Allowed : 26.12 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.31), residues: 789 helix: 1.53 (0.28), residues: 383 sheet: -2.24 (0.57), residues: 64 loop : -1.08 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 388 HIS 0.006 0.001 HIS C 955 PHE 0.013 0.002 PHE C 429 TYR 0.015 0.002 TYR C 703 ARG 0.003 0.000 ARG C 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.002 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.2743 time to fit residues: 29.6251 Evaluate side-chains 74 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1728 time to fit residues: 3.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN C1016 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11130 Z= 0.204 Angle : 0.610 11.687 16014 Z= 0.298 Chirality : 0.036 0.246 1942 Planarity : 0.005 0.059 1316 Dihedral : 23.780 177.614 3837 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 1.04 % Allowed : 25.82 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.31), residues: 789 helix: 1.54 (0.28), residues: 382 sheet: -2.14 (0.58), residues: 64 loop : -1.15 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 388 HIS 0.006 0.001 HIS C 955 PHE 0.015 0.002 PHE C 429 TYR 0.011 0.001 TYR C 703 ARG 0.010 0.000 ARG C 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.920 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.2389 time to fit residues: 26.4919 Evaluate side-chains 73 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1013 time to fit residues: 2.0676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11130 Z= 0.162 Angle : 0.597 11.796 16014 Z= 0.292 Chirality : 0.035 0.226 1942 Planarity : 0.004 0.050 1316 Dihedral : 23.743 177.677 3837 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 0.45 % Allowed : 26.12 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.31), residues: 789 helix: 1.64 (0.28), residues: 382 sheet: -2.01 (0.58), residues: 64 loop : -1.16 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 388 HIS 0.005 0.001 HIS C 955 PHE 0.017 0.002 PHE C 429 TYR 0.008 0.001 TYR C 703 ARG 0.012 0.000 ARG C 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.809 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.2532 time to fit residues: 26.7494 Evaluate side-chains 71 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0984 time to fit residues: 1.2752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11130 Z= 0.151 Angle : 0.585 10.126 16014 Z= 0.287 Chirality : 0.035 0.209 1942 Planarity : 0.004 0.050 1316 Dihedral : 23.717 177.725 3837 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 0.60 % Allowed : 25.52 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.31), residues: 789 helix: 1.72 (0.28), residues: 382 sheet: -1.93 (0.59), residues: 64 loop : -1.08 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 388 HIS 0.005 0.001 HIS C 955 PHE 0.014 0.001 PHE C 429 TYR 0.010 0.001 TYR C 628 ARG 0.003 0.000 ARG C1001 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.914 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.2323 time to fit residues: 25.4085 Evaluate side-chains 74 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0987 time to fit residues: 1.5037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 32 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 68 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.176842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.130230 restraints weight = 22083.129| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 4.83 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11130 Z= 0.144 Angle : 0.583 12.937 16014 Z= 0.283 Chirality : 0.034 0.208 1942 Planarity : 0.004 0.050 1316 Dihedral : 23.680 177.764 3837 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 0.30 % Allowed : 25.97 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 789 helix: 1.75 (0.28), residues: 388 sheet: -1.94 (0.59), residues: 64 loop : -1.07 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 388 HIS 0.006 0.001 HIS C 955 PHE 0.018 0.001 PHE C 429 TYR 0.016 0.001 TYR C 679 ARG 0.003 0.000 ARG C1001 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.56 seconds wall clock time: 36 minutes 33.21 seconds (2193.21 seconds total)