Starting phenix.real_space_refine (version: dev) on Sat Feb 18 07:43:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/02_2023/7ptx_13642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/02_2023/7ptx_13642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/02_2023/7ptx_13642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/02_2023/7ptx_13642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/02_2023/7ptx_13642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/02_2023/7ptx_13642.pdb" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "A ASP 574": "OD1" <-> "OD2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7653 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7653 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 31, 'TRANS': 968} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 156 Time building chain proxies: 4.82, per 1000 atoms: 0.63 Number of scatterers: 7653 At special positions: 0 Unit cell: (123.3, 127.8, 90, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1467 8.00 N 1334 7.00 C 4829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 64.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.585A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.185A pdb=" N GLY A 61 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 62' Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.708A pdb=" N ALA A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 119 through 147 removed outlier: 4.018A pdb=" N GLU A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.506A pdb=" N ILE A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 157 through 178 removed outlier: 3.739A pdb=" N GLU A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 196 through 204 removed outlier: 4.502A pdb=" N SER A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.821A pdb=" N LEU A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 269 Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.750A pdb=" N ARG A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 348 removed outlier: 3.763A pdb=" N ASN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 470 through 484 removed outlier: 4.159A pdb=" N GLY A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 517 through 524 removed outlier: 3.544A pdb=" N LEU A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 541 through 550 removed outlier: 3.878A pdb=" N GLU A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.686A pdb=" N ALA A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 584 Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.975A pdb=" N ILE A 605 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR A 606 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 4.369A pdb=" N ARG A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 Processing helix chain 'A' and resid 642 through 653 removed outlier: 4.250A pdb=" N ASN A 653 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 713 through 723 removed outlier: 4.051A pdb=" N ARG A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 removed outlier: 4.400A pdb=" N ALA A 734 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 745 removed outlier: 3.884A pdb=" N LEU A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 769 through 777 removed outlier: 3.883A pdb=" N LEU A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 789 removed outlier: 4.254A pdb=" N GLN A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 811 removed outlier: 4.173A pdb=" N PHE A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 835 through 844 removed outlier: 3.840A pdb=" N GLU A 839 " --> pdb=" O MET A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 857 removed outlier: 4.094A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 861 Processing helix chain 'A' and resid 870 through 878 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 893 through 897 removed outlier: 3.582A pdb=" N ASN A 897 " --> pdb=" O ASN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 908 removed outlier: 3.753A pdb=" N SER A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 935 through 943 removed outlier: 3.695A pdb=" N PHE A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 955 removed outlier: 4.015A pdb=" N VAL A 949 " --> pdb=" O HIS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 980 removed outlier: 3.741A pdb=" N CYS A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP A 976 " --> pdb=" O HIS A 972 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 999 through 1007 removed outlier: 3.738A pdb=" N GLU A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1054 through 1065 removed outlier: 3.920A pdb=" N VAL A1059 " --> pdb=" O GLU A1055 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A1060 " --> pdb=" O ARG A1056 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A1062 " --> pdb=" O ASP A1058 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 403 388 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 3.28 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: 2577 1.34 - 1.46: 1185 1.46 - 1.58: 3976 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 7777 Sorted by residual: bond pdb=" C ASN A 419 " pdb=" N PRO A 420 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.12e-02 7.97e+03 4.32e+00 bond pdb=" CB PRO A 737 " pdb=" CG PRO A 737 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.30e+00 bond pdb=" C THR A 782 " pdb=" N PRO A 783 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.46e+00 bond pdb=" CG MET A 283 " pdb=" SD MET A 283 " ideal model delta sigma weight residual 1.803 1.778 0.025 2.50e-02 1.60e+03 9.65e-01 bond pdb=" CG GLU A 876 " pdb=" CD GLU A 876 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.64e-01 ... (remaining 7772 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.24: 151 106.24 - 113.17: 4253 113.17 - 120.10: 2783 120.10 - 127.04: 3297 127.04 - 133.97: 53 Bond angle restraints: 10537 Sorted by residual: angle pdb=" CA PRO A 737 " pdb=" N PRO A 737 " pdb=" CD PRO A 737 " ideal model delta sigma weight residual 112.00 106.07 5.93 1.40e+00 5.10e-01 1.79e+01 angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 112.80 108.59 4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" C ILE A 832 " pdb=" N ASN A 833 " pdb=" CA ASN A 833 " ideal model delta sigma weight residual 122.46 127.43 -4.97 1.41e+00 5.03e-01 1.24e+01 angle pdb=" C HIS A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta sigma weight residual 121.14 115.15 5.99 1.75e+00 3.27e-01 1.17e+01 angle pdb=" N GLU A 876 " pdb=" CA GLU A 876 " pdb=" CB GLU A 876 " ideal model delta sigma weight residual 110.39 116.05 -5.66 1.66e+00 3.63e-01 1.16e+01 ... (remaining 10532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 4195 16.46 - 32.91: 441 32.91 - 49.37: 80 49.37 - 65.83: 13 65.83 - 82.28: 7 Dihedral angle restraints: 4736 sinusoidal: 1814 harmonic: 2922 Sorted by residual: dihedral pdb=" CA LYS A 934 " pdb=" C LYS A 934 " pdb=" N SER A 935 " pdb=" CA SER A 935 " ideal model delta harmonic sigma weight residual 180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LYS A 699 " pdb=" C LYS A 699 " pdb=" N ASN A 700 " pdb=" CA ASN A 700 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA THR A 992 " pdb=" C THR A 992 " pdb=" N LEU A 993 " pdb=" CA LEU A 993 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 4733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 719 0.034 - 0.068: 353 0.068 - 0.102: 105 0.102 - 0.135: 36 0.135 - 0.169: 11 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CA GLU A 134 " pdb=" N GLU A 134 " pdb=" C GLU A 134 " pdb=" CB GLU A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA PRO A 737 " pdb=" N PRO A 737 " pdb=" C PRO A 737 " pdb=" CB PRO A 737 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB VAL A 56 " pdb=" CA VAL A 56 " pdb=" CG1 VAL A 56 " pdb=" CG2 VAL A 56 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 1221 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 736 " -0.064 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO A 737 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 737 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 737 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 441 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO A 442 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 442 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 442 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 632 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 633 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.028 5.00e-02 4.00e+02 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 883 2.74 - 3.28: 9100 3.28 - 3.82: 13154 3.82 - 4.36: 15240 4.36 - 4.90: 23646 Nonbonded interactions: 62023 Sorted by model distance: nonbonded pdb=" O PHE A 367 " pdb=" NZ LYS A 407 " model vdw 2.203 2.520 nonbonded pdb=" NH2 ARG A 512 " pdb=" O PHE A 544 " model vdw 2.209 2.520 nonbonded pdb=" O GLU A 493 " pdb=" NZ LYS A 527 " model vdw 2.243 2.520 nonbonded pdb=" O ARG A 610 " pdb=" OG1 THR A 614 " model vdw 2.250 2.440 nonbonded pdb=" O ASN A 439 " pdb=" NZ LYS A 441 " model vdw 2.252 2.520 ... (remaining 62018 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4829 2.51 5 N 1334 2.21 5 O 1467 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 10.680 Check model and map are aligned: 0.130 Process input model: 24.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 0.076 7777 Z= 0.215 Angle : 0.756 8.972 10537 Z= 0.411 Chirality : 0.045 0.169 1224 Planarity : 0.005 0.094 1381 Dihedral : 14.083 82.282 2838 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.26), residues: 994 helix: -0.39 (0.21), residues: 575 sheet: -3.62 (0.77), residues: 35 loop : -2.46 (0.30), residues: 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1822 time to fit residues: 30.0123 Evaluate side-chains 89 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 42 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7777 Z= 0.178 Angle : 0.634 6.727 10537 Z= 0.333 Chirality : 0.042 0.151 1224 Planarity : 0.005 0.058 1381 Dihedral : 5.423 21.111 1058 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 994 helix: -0.01 (0.21), residues: 584 sheet: -3.37 (0.78), residues: 35 loop : -2.37 (0.30), residues: 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.887 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.1883 time to fit residues: 32.7603 Evaluate side-chains 91 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7777 Z= 0.224 Angle : 0.651 5.936 10537 Z= 0.348 Chirality : 0.044 0.154 1224 Planarity : 0.005 0.055 1381 Dihedral : 5.519 21.357 1058 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 994 helix: -0.01 (0.21), residues: 583 sheet: -3.20 (0.83), residues: 35 loop : -2.40 (0.30), residues: 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 122 average time/residue: 0.1933 time to fit residues: 34.3653 Evaluate side-chains 89 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.0060 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 HIS A 897 ASN A 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7777 Z= 0.188 Angle : 0.653 7.273 10537 Z= 0.341 Chirality : 0.043 0.151 1224 Planarity : 0.004 0.053 1381 Dihedral : 5.415 21.563 1058 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 994 helix: 0.18 (0.22), residues: 575 sheet: -2.63 (0.89), residues: 33 loop : -2.34 (0.30), residues: 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 126 average time/residue: 0.2060 time to fit residues: 35.4395 Evaluate side-chains 89 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0783 time to fit residues: 1.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7777 Z= 0.184 Angle : 0.663 7.907 10537 Z= 0.345 Chirality : 0.044 0.156 1224 Planarity : 0.005 0.060 1381 Dihedral : 5.359 21.092 1058 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 994 helix: 0.17 (0.22), residues: 575 sheet: -2.24 (0.93), residues: 33 loop : -2.31 (0.30), residues: 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.970 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1928 time to fit residues: 34.3601 Evaluate side-chains 88 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7777 Z= 0.213 Angle : 0.680 7.905 10537 Z= 0.354 Chirality : 0.044 0.165 1224 Planarity : 0.004 0.052 1381 Dihedral : 5.402 21.375 1058 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.26), residues: 994 helix: 0.09 (0.21), residues: 575 sheet: -1.91 (0.99), residues: 31 loop : -2.28 (0.30), residues: 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1904 time to fit residues: 32.4329 Evaluate side-chains 88 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.0170 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 7777 Z= 0.208 Angle : 0.684 8.543 10537 Z= 0.354 Chirality : 0.044 0.186 1224 Planarity : 0.004 0.052 1381 Dihedral : 5.334 21.378 1058 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 994 helix: 0.12 (0.21), residues: 582 sheet: -1.68 (1.02), residues: 31 loop : -2.30 (0.30), residues: 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.862 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2060 time to fit residues: 34.7198 Evaluate side-chains 88 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 7777 Z= 0.206 Angle : 0.698 8.643 10537 Z= 0.360 Chirality : 0.045 0.205 1224 Planarity : 0.004 0.051 1381 Dihedral : 5.316 21.422 1058 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 994 helix: 0.11 (0.21), residues: 582 sheet: -1.51 (1.02), residues: 31 loop : -2.31 (0.30), residues: 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1886 time to fit residues: 30.9381 Evaluate side-chains 85 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 7777 Z= 0.207 Angle : 0.712 9.016 10537 Z= 0.366 Chirality : 0.045 0.177 1224 Planarity : 0.004 0.051 1381 Dihedral : 5.331 21.758 1058 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 994 helix: 0.07 (0.21), residues: 583 sheet: -1.34 (1.03), residues: 31 loop : -2.32 (0.30), residues: 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.637 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2125 time to fit residues: 34.6600 Evaluate side-chains 87 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 24 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 7777 Z= 0.203 Angle : 0.714 9.475 10537 Z= 0.364 Chirality : 0.045 0.207 1224 Planarity : 0.004 0.051 1381 Dihedral : 5.278 21.610 1058 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 994 helix: 0.12 (0.21), residues: 583 sheet: -0.50 (1.31), residues: 23 loop : -2.29 (0.30), residues: 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.002 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1905 time to fit residues: 31.2750 Evaluate side-chains 89 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0170 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 0.0980 chunk 69 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.081657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.069891 restraints weight = 42875.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.071540 restraints weight = 28378.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.072691 restraints weight = 20615.241| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 7777 Z= 0.190 Angle : 0.735 10.194 10537 Z= 0.368 Chirality : 0.045 0.219 1224 Planarity : 0.004 0.051 1381 Dihedral : 5.176 21.403 1058 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.26), residues: 994 helix: 0.11 (0.21), residues: 585 sheet: -1.43 (1.04), residues: 33 loop : -2.19 (0.31), residues: 376 =============================================================================== Job complete usr+sys time: 1867.98 seconds wall clock time: 34 minutes 58.70 seconds (2098.70 seconds total)