Starting phenix.real_space_refine on Sat Apr 6 08:56:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9t_36997/04_2024/8k9t_36997_neut_updated.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 33 5.16 5 C 5046 2.51 5 N 1276 2.21 5 O 1389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7747 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7520 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 61, 'TRANS': 899} Chain breaks: 3 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'05E': 1, 'CLR': 2, 'LYI': 1, 'MAN': 2, 'PA1': 1, 'PLM': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'80Y': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.86, per 1000 atoms: 0.63 Number of scatterers: 7747 At special positions: 0 Unit cell: (79.22, 91.336, 134.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 3 15.00 O 1389 8.00 N 1276 7.00 C 5046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 449 " distance=2.04 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 606 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 793 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 5 sheets defined 41.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 147 through 169 removed outlier: 3.552A pdb=" N VAL A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.718A pdb=" N SER A 201 " --> pdb=" O ARG A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.755A pdb=" N VAL A 237 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.612A pdb=" N GLU A 243 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 247 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 248 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 282 through 304 removed outlier: 3.771A pdb=" N TYR A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.612A pdb=" N ALA A 333 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 445 through 448 No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 645 through 648 No H-bonds generated for 'chain 'A' and resid 645 through 648' Processing helix chain 'A' and resid 675 through 678 No H-bonds generated for 'chain 'A' and resid 675 through 678' Processing helix chain 'A' and resid 686 through 692 Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 805 through 821 removed outlier: 4.049A pdb=" N LEU A 812 " --> pdb=" O SER A 808 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N MET A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR A 818 " --> pdb=" O MET A 814 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA A 821 " --> pdb=" O ARG A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 removed outlier: 3.650A pdb=" N VAL A 828 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 829 " --> pdb=" O PHE A 826 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 832 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 835 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 838 " --> pdb=" O GLN A 835 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 842 " --> pdb=" O TYR A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 857 removed outlier: 3.614A pdb=" N ARG A 857 " --> pdb=" O ASP A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 871 Processing helix chain 'A' and resid 909 through 953 removed outlier: 4.383A pdb=" N PHE A 913 " --> pdb=" O PHE A 910 " (cutoff:3.500A) Proline residue: A 916 - end of helix removed outlier: 3.886A pdb=" N ARG A 953 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 992 removed outlier: 3.648A pdb=" N VAL A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 992 " --> pdb=" O PHE A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 986 through 992' Processing helix chain 'A' and resid 996 through 1021 Processing helix chain 'A' and resid 1024 through 1060 removed outlier: 3.694A pdb=" N ILE A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A1044 " --> pdb=" O MET A1040 " (cutoff:3.500A) Proline residue: A1045 - end of helix Proline residue: A1049 - end of helix Processing helix chain 'A' and resid 1068 through 1086 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1103 through 1124 removed outlier: 3.672A pdb=" N THR A1110 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A1111 " --> pdb=" O ARG A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1147 Processing sheet with id= A, first strand: chain 'A' and resid 186 through 188 removed outlier: 4.968A pdb=" N PHE A 268 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 222 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N PHE A 269 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 224 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 271 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 226 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 322 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE A 227 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 324 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN A 348 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 323 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 350 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY A 325 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR A 352 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR A 397 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR A 352 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 399 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 427 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 591 through 594 Processing sheet with id= C, first strand: chain 'A' and resid 523 through 525 Processing sheet with id= D, first strand: chain 'A' and resid 679 through 681 removed outlier: 8.316A pdb=" N HIS A 680 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU A 707 " --> pdb=" O HIS A 680 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 749 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 694 through 698 removed outlier: 4.580A pdb=" N ALA A 719 " --> pdb=" O ASP A 804 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 750 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: 2.49 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1180 1.30 - 1.43: 2111 1.43 - 1.56: 4600 1.56 - 1.68: 7 1.68 - 1.81: 55 Bond restraints: 7953 Sorted by residual: bond pdb=" OA5 LYI A1506 " pdb=" PA6 LYI A1506 " ideal model delta sigma weight residual 1.666 1.554 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" OA7 LYI A1506 " pdb=" PA6 LYI A1506 " ideal model delta sigma weight residual 1.669 1.567 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O84 05E A1504 " pdb=" P83 05E A1504 " ideal model delta sigma weight residual 1.678 1.577 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" CA ILE A 508 " pdb=" C ILE A 508 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.43e+01 bond pdb=" C PRO A 909 " pdb=" O PRO A 909 " ideal model delta sigma weight residual 1.238 1.179 0.059 1.24e-02 6.50e+03 2.24e+01 ... (remaining 7948 not shown) Histogram of bond angle deviations from ideal: 96.85 - 104.36: 200 104.36 - 111.88: 4059 111.88 - 119.40: 2620 119.40 - 126.91: 3842 126.91 - 134.43: 137 Bond angle restraints: 10858 Sorted by residual: angle pdb=" N ALA A1150 " pdb=" CA ALA A1150 " pdb=" C ALA A1150 " ideal model delta sigma weight residual 113.16 99.51 13.65 1.24e+00 6.50e-01 1.21e+02 angle pdb=" CC4 LYI A1506 " pdb=" CC5 LYI A1506 " pdb=" CC6 LYI A1506 " ideal model delta sigma weight residual 152.66 125.28 27.38 3.00e+00 1.11e-01 8.33e+01 angle pdb=" CB5 LYI A1506 " pdb=" CB6 LYI A1506 " pdb=" CB7 LYI A1506 " ideal model delta sigma weight residual 152.65 128.20 24.45 3.00e+00 1.11e-01 6.64e+01 angle pdb=" CB8 LYI A1506 " pdb=" CB9 LYI A1506 " pdb=" CC0 LYI A1506 " ideal model delta sigma weight residual 152.66 128.39 24.27 3.00e+00 1.11e-01 6.55e+01 angle pdb=" C ASN A 230 " pdb=" N ALA A 231 " pdb=" CA ALA A 231 " ideal model delta sigma weight residual 122.40 131.96 -9.56 1.45e+00 4.76e-01 4.35e+01 ... (remaining 10853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 4749 35.21 - 70.42: 108 70.42 - 105.63: 9 105.63 - 140.85: 13 140.85 - 176.06: 2 Dihedral angle restraints: 4881 sinusoidal: 2050 harmonic: 2831 Sorted by residual: dihedral pdb=" C THR A1149 " pdb=" N THR A1149 " pdb=" CA THR A1149 " pdb=" CB THR A1149 " ideal model delta harmonic sigma weight residual -122.00 -138.25 16.25 0 2.50e+00 1.60e-01 4.23e+01 dihedral pdb=" CA GLU A 746 " pdb=" C GLU A 746 " pdb=" N PRO A 747 " pdb=" CA PRO A 747 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" N THR A1149 " pdb=" C THR A1149 " pdb=" CA THR A1149 " pdb=" CB THR A1149 " ideal model delta harmonic sigma weight residual 123.40 136.48 -13.08 0 2.50e+00 1.60e-01 2.74e+01 ... (remaining 4878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.015: 1280 1.015 - 2.030: 0 2.030 - 3.046: 0 3.046 - 4.061: 0 4.061 - 5.076: 2 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA4 LYI A1506 " pdb=" C3 LYI A1506 " pdb=" C9 LYI A1506 " pdb=" OA5 LYI A1506 " both_signs ideal model delta sigma weight residual False -2.53 2.55 -5.08 2.00e-01 2.50e+01 6.44e+02 chirality pdb=" C5 LYI A1506 " pdb=" C2 LYI A1506 " pdb=" C7 LYI A1506 " pdb=" O6 LYI A1506 " both_signs ideal model delta sigma weight residual False -2.51 2.47 -4.99 2.00e-01 2.50e+01 6.22e+02 chirality pdb=" CA THR A1149 " pdb=" N THR A1149 " pdb=" C THR A1149 " pdb=" CB THR A1149 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 1279 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 229 " -0.020 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C GLY A 229 " 0.065 2.00e-02 2.50e+03 pdb=" O GLY A 229 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN A 230 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 379 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" CG TRP A 379 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 379 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 379 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 379 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 379 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 379 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 379 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 379 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 379 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 330 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLY A 330 " 0.056 2.00e-02 2.50e+03 pdb=" O GLY A 330 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 331 " -0.019 2.00e-02 2.50e+03 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1825 2.79 - 3.32: 7214 3.32 - 3.84: 13207 3.84 - 4.37: 16350 4.37 - 4.90: 27318 Nonbonded interactions: 65914 Sorted by model distance: nonbonded pdb=" NH2 ARG A 178 " pdb=" OE2 GLU A 634 " model vdw 2.261 2.520 nonbonded pdb=" OG SER A 716 " pdb=" NH2 ARG A 815 " model vdw 2.299 2.520 nonbonded pdb=" NH1 ARG A 741 " pdb=" OE1 GLN A 786 " model vdw 2.316 2.520 nonbonded pdb=" NE2 GLN A 835 " pdb=" O ILE A 846 " model vdw 2.334 2.520 nonbonded pdb=" OD2 ASP A 442 " pdb=" O4 MAN A1502 " model vdw 2.347 2.440 ... (remaining 65909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.010 Extract box with map and model: 4.650 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.990 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.112 7953 Z= 0.627 Angle : 1.101 27.384 10858 Z= 0.609 Chirality : 0.207 5.076 1282 Planarity : 0.006 0.063 1339 Dihedral : 16.689 176.057 3034 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % Rotamer: Outliers : 0.97 % Allowed : 1.57 % Favored : 97.46 % Cbeta Deviations : 0.22 % 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: 0.46 (0.26), residues: 955 helix: 0.70 (0.26), residues: 369 sheet: 1.20 (0.43), residues: 147 loop : -0.26 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A 379 HIS 0.009 0.001 HIS A 443 PHE 0.046 0.002 PHE A 845 TYR 0.013 0.002 TYR A 743 ARG 0.007 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 175 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8178 (mtpp) REVERT: A 188 LYS cc_start: 0.8378 (ttpp) cc_final: 0.8113 (ttmm) REVERT: A 275 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: A 346 SER cc_start: 0.8838 (t) cc_final: 0.8599 (p) REVERT: A 386 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7857 (ptmt) REVERT: A 484 LYS cc_start: 0.7862 (tppt) cc_final: 0.7390 (tttm) REVERT: A 550 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7607 (mttp) REVERT: A 568 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7871 (mtmm) REVERT: A 570 GLU cc_start: 0.7535 (tt0) cc_final: 0.7308 (tt0) REVERT: A 697 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7630 (ttm-80) REVERT: A 723 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.7352 (ttm170) REVERT: A 774 MET cc_start: 0.7600 (ttm) cc_final: 0.6455 (mpt) REVERT: A 781 GLU cc_start: 0.7692 (pt0) cc_final: 0.7322 (mm-30) REVERT: A 871 THR cc_start: 0.8439 (m) cc_final: 0.8191 (m) REVERT: A 1013 ARG cc_start: 0.6745 (ttm170) cc_final: 0.5894 (ttt-90) REVERT: A 1015 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7930 (tm-30) outliers start: 8 outliers final: 4 residues processed: 142 average time/residue: 1.3466 time to fit residues: 201.7033 Evaluate side-chains 94 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 HIS A 608 ASN A 794 ASN A 798 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7953 Z= 0.225 Angle : 0.616 10.080 10858 Z= 0.305 Chirality : 0.048 0.417 1282 Planarity : 0.006 0.055 1339 Dihedral : 14.237 178.719 1329 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.88 % Favored : 98.01 % Rotamer: Outliers : 1.45 % Allowed : 7.62 % Favored : 90.93 % 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: 0.86 (0.27), residues: 955 helix: 1.13 (0.26), residues: 363 sheet: 0.92 (0.41), residues: 157 loop : 0.07 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 379 HIS 0.004 0.001 HIS A 898 PHE 0.014 0.001 PHE A 845 TYR 0.013 0.001 TYR A 839 ARG 0.007 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.910 Fit side-chains REVERT: A 256 GLU cc_start: 0.7143 (tt0) cc_final: 0.6679 (pp20) REVERT: A 276 ASP cc_start: 0.7584 (m-30) cc_final: 0.7144 (m-30) REVERT: A 346 SER cc_start: 0.8834 (t) cc_final: 0.8619 (p) REVERT: A 386 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7823 (ptmt) REVERT: A 484 LYS cc_start: 0.7844 (tppt) cc_final: 0.7387 (tttm) REVERT: A 521 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6778 (mm-30) REVERT: A 550 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7672 (mttp) REVERT: A 568 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7769 (mtpm) REVERT: A 570 GLU cc_start: 0.7617 (tt0) cc_final: 0.7404 (tt0) REVERT: A 621 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7222 (mtm-85) REVERT: A 676 SER cc_start: 0.8346 (m) cc_final: 0.8021 (p) REVERT: A 774 MET cc_start: 0.7580 (ttm) cc_final: 0.6574 (mpt) REVERT: A 781 GLU cc_start: 0.7668 (pt0) cc_final: 0.7274 (mm-30) REVERT: A 1013 ARG cc_start: 0.6778 (ttm170) cc_final: 0.5904 (ttp-170) outliers start: 12 outliers final: 6 residues processed: 120 average time/residue: 1.2593 time to fit residues: 160.3055 Evaluate side-chains 102 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN A 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7953 Z= 0.190 Angle : 0.544 7.600 10858 Z= 0.271 Chirality : 0.043 0.249 1282 Planarity : 0.005 0.051 1339 Dihedral : 12.803 166.188 1322 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.12 % Rotamer: Outliers : 1.33 % Allowed : 10.16 % Favored : 88.51 % 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: 0.93 (0.27), residues: 955 helix: 1.14 (0.27), residues: 362 sheet: 0.62 (0.39), residues: 173 loop : 0.31 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1153 HIS 0.005 0.001 HIS A 443 PHE 0.009 0.001 PHE A 452 TYR 0.009 0.001 TYR A 743 ARG 0.005 0.000 ARG A 938 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.707 Fit side-chains REVERT: A 179 MET cc_start: 0.9199 (tpp) cc_final: 0.8964 (tpt) REVERT: A 256 GLU cc_start: 0.6988 (tt0) cc_final: 0.6595 (pp20) REVERT: A 386 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7753 (ptmt) REVERT: A 484 LYS cc_start: 0.7969 (tppt) cc_final: 0.7494 (tttm) REVERT: A 550 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7665 (mttp) REVERT: A 568 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7819 (mtpm) REVERT: A 774 MET cc_start: 0.7607 (ttm) cc_final: 0.6543 (mpt) REVERT: A 781 GLU cc_start: 0.7700 (pt0) cc_final: 0.7303 (mm-30) REVERT: A 903 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7922 (tt) REVERT: A 1013 ARG cc_start: 0.6753 (ttm170) cc_final: 0.5865 (ttp-170) REVERT: A 1079 ILE cc_start: 0.8083 (mm) cc_final: 0.7873 (mt) outliers start: 11 outliers final: 4 residues processed: 118 average time/residue: 1.3314 time to fit residues: 166.1736 Evaluate side-chains 106 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 444 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7953 Z= 0.224 Angle : 0.534 7.212 10858 Z= 0.268 Chirality : 0.042 0.179 1282 Planarity : 0.005 0.051 1339 Dihedral : 12.012 161.568 1322 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % Rotamer: Outliers : 1.81 % Allowed : 11.25 % Favored : 86.94 % 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: 0.96 (0.28), residues: 955 helix: 1.11 (0.28), residues: 363 sheet: 0.39 (0.38), residues: 188 loop : 0.51 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 448 HIS 0.007 0.001 HIS A 443 PHE 0.009 0.001 PHE A 452 TYR 0.010 0.001 TYR A 743 ARG 0.012 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.876 Fit side-chains REVERT: A 140 ARG cc_start: 0.7720 (ttt180) cc_final: 0.7464 (ttt180) REVERT: A 179 MET cc_start: 0.9232 (tpp) cc_final: 0.9023 (tpt) REVERT: A 256 GLU cc_start: 0.6917 (tt0) cc_final: 0.6598 (pp20) REVERT: A 386 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7747 (ptmt) REVERT: A 484 LYS cc_start: 0.7966 (tppt) cc_final: 0.7526 (tttm) REVERT: A 521 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6658 (tt0) REVERT: A 550 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7530 (mttp) REVERT: A 568 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7867 (mtpm) REVERT: A 621 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7434 (mtm-85) REVERT: A 774 MET cc_start: 0.7631 (ttm) cc_final: 0.6532 (mpt) REVERT: A 781 GLU cc_start: 0.7738 (pt0) cc_final: 0.7291 (mm-30) REVERT: A 903 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 994 ILE cc_start: 0.8266 (mm) cc_final: 0.7875 (tt) REVERT: A 1013 ARG cc_start: 0.6757 (ttm170) cc_final: 0.5839 (ttp-170) REVERT: A 1076 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7353 (mmm) REVERT: A 1079 ILE cc_start: 0.8067 (mm) cc_final: 0.7834 (mt) outliers start: 15 outliers final: 6 residues processed: 114 average time/residue: 1.3571 time to fit residues: 163.3568 Evaluate side-chains 103 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 1076 MET Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 389 ASN A1047 ASN A1089 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7953 Z= 0.326 Angle : 0.570 7.328 10858 Z= 0.287 Chirality : 0.044 0.206 1282 Planarity : 0.005 0.051 1339 Dihedral : 12.080 163.383 1322 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % Rotamer: Outliers : 1.57 % Allowed : 11.61 % Favored : 86.82 % 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: 0.89 (0.28), residues: 955 helix: 0.98 (0.27), residues: 364 sheet: 0.44 (0.38), residues: 186 loop : 0.52 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 448 HIS 0.005 0.001 HIS A 443 PHE 0.012 0.001 PHE A 452 TYR 0.010 0.002 TYR A 996 ARG 0.003 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.921 Fit side-chains REVERT: A 484 LYS cc_start: 0.7979 (tppt) cc_final: 0.7527 (tttm) REVERT: A 521 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6706 (tt0) REVERT: A 568 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7898 (mttm) REVERT: A 645 LEU cc_start: 0.7958 (tp) cc_final: 0.7694 (tp) REVERT: A 696 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 774 MET cc_start: 0.7745 (ttm) cc_final: 0.6503 (mpt) REVERT: A 781 GLU cc_start: 0.7744 (pt0) cc_final: 0.7292 (mm-30) REVERT: A 903 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7877 (tt) REVERT: A 1013 ARG cc_start: 0.6750 (ttm170) cc_final: 0.5859 (ttp-170) REVERT: A 1079 ILE cc_start: 0.8088 (mm) cc_final: 0.7856 (mt) outliers start: 13 outliers final: 5 residues processed: 102 average time/residue: 1.3952 time to fit residues: 150.3328 Evaluate side-chains 97 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 0.0570 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 389 ASN A1047 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7953 Z= 0.187 Angle : 0.510 6.957 10858 Z= 0.257 Chirality : 0.041 0.174 1282 Planarity : 0.005 0.049 1339 Dihedral : 11.679 155.179 1322 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.12 % Rotamer: Outliers : 1.69 % Allowed : 12.58 % Favored : 85.73 % 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: 0.92 (0.28), residues: 955 helix: 1.02 (0.27), residues: 370 sheet: 0.39 (0.38), residues: 187 loop : 0.54 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 448 HIS 0.005 0.000 HIS A 443 PHE 0.008 0.001 PHE A 452 TYR 0.010 0.001 TYR A 743 ARG 0.012 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.843 Fit side-chains REVERT: A 484 LYS cc_start: 0.7958 (tppt) cc_final: 0.7536 (tttm) REVERT: A 521 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6664 (tt0) REVERT: A 568 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7825 (mtpm) REVERT: A 621 ARG cc_start: 0.7734 (mtm110) cc_final: 0.7469 (mtm-85) REVERT: A 774 MET cc_start: 0.7750 (ttm) cc_final: 0.6538 (mpt) REVERT: A 781 GLU cc_start: 0.7739 (pt0) cc_final: 0.7274 (mm-30) REVERT: A 903 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 1013 ARG cc_start: 0.6729 (ttm170) cc_final: 0.5840 (ttp-170) REVERT: A 1076 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7464 (mmm) REVERT: A 1079 ILE cc_start: 0.8071 (mm) cc_final: 0.7838 (mt) outliers start: 14 outliers final: 7 residues processed: 103 average time/residue: 1.4065 time to fit residues: 152.8193 Evaluate side-chains 99 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7953 Z= 0.190 Angle : 0.503 6.850 10858 Z= 0.253 Chirality : 0.041 0.167 1282 Planarity : 0.005 0.048 1339 Dihedral : 11.704 161.240 1321 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % Rotamer: Outliers : 1.33 % Allowed : 13.66 % Favored : 85.01 % 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: 0.97 (0.28), residues: 955 helix: 1.08 (0.27), residues: 370 sheet: 0.40 (0.38), residues: 187 loop : 0.54 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1042 HIS 0.004 0.000 HIS A 443 PHE 0.008 0.001 PHE A 452 TYR 0.009 0.001 TYR A 743 ARG 0.009 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.934 Fit side-chains REVERT: A 484 LYS cc_start: 0.7959 (tppt) cc_final: 0.7537 (tttm) REVERT: A 521 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6635 (tt0) REVERT: A 568 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7942 (mtpp) REVERT: A 624 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7479 (ttp80) REVERT: A 774 MET cc_start: 0.7737 (ttm) cc_final: 0.6509 (mpt) REVERT: A 781 GLU cc_start: 0.7743 (pt0) cc_final: 0.7277 (mm-30) REVERT: A 903 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 1013 ARG cc_start: 0.6748 (ttm170) cc_final: 0.5840 (ttp-170) REVERT: A 1076 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7449 (mmm) REVERT: A 1079 ILE cc_start: 0.8073 (mm) cc_final: 0.7849 (mt) outliers start: 11 outliers final: 7 residues processed: 100 average time/residue: 1.3600 time to fit residues: 143.8831 Evaluate side-chains 100 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.0270 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 389 ASN A 837 GLN A1056 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7953 Z= 0.164 Angle : 0.494 7.278 10858 Z= 0.247 Chirality : 0.041 0.156 1282 Planarity : 0.005 0.050 1339 Dihedral : 11.631 163.705 1321 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % Rotamer: Outliers : 1.09 % Allowed : 14.51 % Favored : 84.40 % 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: 1.02 (0.28), residues: 955 helix: 1.19 (0.28), residues: 370 sheet: 0.42 (0.38), residues: 187 loop : 0.51 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 448 HIS 0.004 0.000 HIS A 443 PHE 0.007 0.001 PHE A 452 TYR 0.009 0.001 TYR A 743 ARG 0.013 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.913 Fit side-chains REVERT: A 484 LYS cc_start: 0.8082 (tppt) cc_final: 0.7593 (tttm) REVERT: A 521 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6627 (tt0) REVERT: A 568 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7970 (mtpp) REVERT: A 621 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7515 (mtm-85) REVERT: A 624 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7491 (ttp80) REVERT: A 630 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7389 (mmm-85) REVERT: A 734 ASP cc_start: 0.8261 (p0) cc_final: 0.8055 (p0) REVERT: A 774 MET cc_start: 0.7655 (ttm) cc_final: 0.6493 (mpt) REVERT: A 781 GLU cc_start: 0.7721 (pt0) cc_final: 0.7300 (mm-30) REVERT: A 903 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7871 (tt) REVERT: A 1013 ARG cc_start: 0.6750 (ttm170) cc_final: 0.5827 (ttp-170) REVERT: A 1076 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7450 (mmm) REVERT: A 1079 ILE cc_start: 0.8062 (mm) cc_final: 0.7843 (mt) outliers start: 9 outliers final: 2 residues processed: 102 average time/residue: 1.4335 time to fit residues: 154.3918 Evaluate side-chains 98 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 837 GLN A1056 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7953 Z= 0.188 Angle : 0.492 6.675 10858 Z= 0.249 Chirality : 0.041 0.158 1282 Planarity : 0.005 0.049 1339 Dihedral : 11.640 164.835 1321 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 1.09 % Allowed : 13.78 % Favored : 85.13 % 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: 1.04 (0.28), residues: 955 helix: 1.21 (0.28), residues: 370 sheet: 0.42 (0.38), residues: 186 loop : 0.51 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 448 HIS 0.003 0.000 HIS A 443 PHE 0.008 0.001 PHE A 452 TYR 0.009 0.001 TYR A 743 ARG 0.010 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.879 Fit side-chains REVERT: A 304 LEU cc_start: 0.8355 (mt) cc_final: 0.8140 (mp) REVERT: A 348 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.7520 (p0) REVERT: A 484 LYS cc_start: 0.8096 (tppt) cc_final: 0.7600 (tttm) REVERT: A 521 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6638 (tt0) REVERT: A 568 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7972 (mtpp) REVERT: A 621 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7499 (mtm-85) REVERT: A 624 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7366 (ttp80) REVERT: A 630 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7407 (mmm-85) REVERT: A 734 ASP cc_start: 0.8290 (p0) cc_final: 0.8080 (p0) REVERT: A 774 MET cc_start: 0.7649 (ttm) cc_final: 0.6479 (mpt) REVERT: A 781 GLU cc_start: 0.7721 (pt0) cc_final: 0.7305 (mm-30) REVERT: A 903 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7798 (tt) REVERT: A 1013 ARG cc_start: 0.6755 (ttm170) cc_final: 0.5829 (ttp-170) REVERT: A 1076 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7436 (mmm) REVERT: A 1079 ILE cc_start: 0.8076 (mm) cc_final: 0.7862 (mt) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 1.4505 time to fit residues: 157.6047 Evaluate side-chains 103 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.0060 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 837 GLN A1056 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7953 Z= 0.152 Angle : 0.480 6.535 10858 Z= 0.242 Chirality : 0.040 0.150 1282 Planarity : 0.005 0.048 1339 Dihedral : 11.456 160.716 1321 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.88 % Favored : 98.01 % Rotamer: Outliers : 0.85 % Allowed : 14.51 % Favored : 84.64 % 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: 1.08 (0.28), residues: 955 helix: 1.25 (0.28), residues: 370 sheet: 0.44 (0.38), residues: 187 loop : 0.53 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 448 HIS 0.004 0.000 HIS A 443 PHE 0.006 0.001 PHE A 820 TYR 0.009 0.001 TYR A 743 ARG 0.011 0.000 ARG A 621 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.979 Fit side-chains REVERT: A 484 LYS cc_start: 0.8084 (tppt) cc_final: 0.7603 (tttm) REVERT: A 521 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6682 (tt0) REVERT: A 568 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7970 (mtpp) REVERT: A 621 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7506 (mtm-85) REVERT: A 624 ARG cc_start: 0.7679 (mtm110) cc_final: 0.7361 (ttp80) REVERT: A 630 ARG cc_start: 0.7607 (mtm110) cc_final: 0.7404 (mmm-85) REVERT: A 697 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7197 (tpt170) REVERT: A 734 ASP cc_start: 0.8270 (p0) cc_final: 0.8068 (p0) REVERT: A 774 MET cc_start: 0.7641 (ttm) cc_final: 0.6485 (mpt) REVERT: A 781 GLU cc_start: 0.7721 (pt0) cc_final: 0.7304 (mm-30) REVERT: A 903 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7817 (tt) REVERT: A 1013 ARG cc_start: 0.6732 (ttm170) cc_final: 0.5805 (ttp-170) REVERT: A 1076 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7446 (mmm) REVERT: A 1079 ILE cc_start: 0.8066 (mm) cc_final: 0.7864 (mt) outliers start: 7 outliers final: 2 residues processed: 107 average time/residue: 1.3579 time to fit residues: 153.7212 Evaluate side-chains 99 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 837 GLN A1047 ASN A1056 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100293 restraints weight = 9147.685| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.08 r_work: 0.3124 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7953 Z= 0.194 Angle : 0.502 6.853 10858 Z= 0.252 Chirality : 0.041 0.155 1282 Planarity : 0.005 0.048 1339 Dihedral : 11.526 162.201 1321 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % Rotamer: Outliers : 0.85 % Allowed : 14.99 % Favored : 84.16 % 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: 1.06 (0.28), residues: 955 helix: 1.23 (0.27), residues: 370 sheet: 0.49 (0.38), residues: 186 loop : 0.50 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 448 HIS 0.003 0.000 HIS A 443 PHE 0.008 0.001 PHE A 820 TYR 0.009 0.001 TYR A 996 ARG 0.010 0.000 ARG A 621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.98 seconds wall clock time: 60 minutes 32.32 seconds (3632.32 seconds total)