Starting phenix.real_space_refine on Sat Dec 9 05:56:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/12_2023/8sea_40408_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/12_2023/8sea_40408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/12_2023/8sea_40408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/12_2023/8sea_40408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/12_2023/8sea_40408_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/12_2023/8sea_40408_updated.pdb" } resolution = 3.4 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= 0.020 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 1 5.49 5 S 37 5.16 5 C 6490 2.51 5 N 1792 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7712 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 926} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLY%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 5.94, per 1000 atoms: 0.58 Number of scatterers: 10208 At special positions: 0 Unit cell: (91.652, 104.983, 117.481, 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 37 16.00 P 1 15.00 O 1888 8.00 N 1792 7.00 C 6490 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.9 seconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 13 sheets defined 37.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 4.059A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 87 through 98 removed outlier: 4.077A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 267 through 272 removed outlier: 4.330A pdb=" N LEU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 304 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 405 through 408 No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 removed outlier: 4.640A pdb=" N VAL A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 518 through 520 No H-bonds generated for 'chain 'A' and resid 518 through 520' Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 542 through 555 Processing helix chain 'A' and resid 586 through 593 removed outlier: 4.306A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 608 through 630 removed outlier: 3.870A pdb=" N LEU A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 645 through 650 Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 671 through 680 removed outlier: 4.092A pdb=" N GLY A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 722 through 739 Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'A' and resid 783 through 799 Processing helix chain 'A' and resid 818 through 831 Processing helix chain 'A' and resid 839 through 844 Processing helix chain 'A' and resid 854 through 873 Processing helix chain 'A' and resid 878 through 880 No H-bonds generated for 'chain 'A' and resid 878 through 880' Processing helix chain 'A' and resid 928 through 939 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.701A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'D' and resid 104 through 115 removed outlier: 3.760A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 137 through 140 No H-bonds generated for 'chain 'D' and resid 137 through 140' Processing sheet with id= A, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.717A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER A 58 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL A 37 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 60 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 103 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A 61 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 105 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.923A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 166 through 168 Processing sheet with id= D, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.492A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 534 through 537 removed outlier: 7.258A pdb=" N ALA A 537 " --> pdb=" O PRO A 558 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU A 560 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 904 through 906 Processing sheet with id= G, first strand: chain 'A' and resid 917 through 919 removed outlier: 3.648A pdb=" N GLU A1011 " --> pdb=" O VAL A 919 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 181 through 184 removed outlier: 6.601A pdb=" N THR A 193 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 214 through 216 Processing sheet with id= J, first strand: chain 'A' and resid 945 through 948 removed outlier: 3.515A pdb=" N TYR A 954 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU A 952 " --> pdb=" O HIS A 948 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 93 through 98 Processing sheet with id= L, first strand: chain 'C' and resid 34 through 39 Processing sheet with id= M, first strand: chain 'D' and resid 122 through 126 removed outlier: 4.323A pdb=" N TRP D 123 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN D 151 " --> pdb=" O TRP D 123 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 125 " --> pdb=" O PHE D 149 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 996 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: 3.40 Time building geometry restraints manager: 4.36 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: 3420 1.34 - 1.46: 1327 1.46 - 1.57: 5653 1.57 - 1.69: 4 1.69 - 1.81: 56 Bond restraints: 10460 Sorted by residual: bond pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.415 1.624 -0.209 1.50e-02 4.44e+03 1.94e+02 bond pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " ideal model delta sigma weight residual 1.526 1.366 0.160 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.454 1.295 0.159 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C6 AMP B1101 " pdb=" N6 AMP B1101 " ideal model delta sigma weight residual 1.355 1.497 -0.142 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 AMP B1101 " pdb=" C5 AMP B1101 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 10455 not shown) Histogram of bond angle deviations from ideal: 95.38 - 103.21: 128 103.21 - 111.04: 4180 111.04 - 118.87: 4384 118.87 - 126.70: 5343 126.70 - 134.54: 207 Bond angle restraints: 14242 Sorted by residual: angle pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" N9 AMP B1101 " ideal model delta sigma weight residual 114.00 127.43 -13.43 1.50e+00 4.44e-01 8.02e+01 angle pdb=" N9 AMP B1101 " pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 108.20 95.38 12.82 1.50e+00 4.44e-01 7.30e+01 angle pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C4' AMP B1101 " ideal model delta sigma weight residual 109.70 104.33 5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" O2P AMP B1101 " pdb=" P AMP B1101 " pdb=" O3P AMP B1101 " ideal model delta sigma weight residual 119.90 106.37 13.53 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C3' AMP B1101 " ideal model delta sigma weight residual 101.50 105.75 -4.25 1.00e+00 1.00e+00 1.81e+01 ... (remaining 14237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 5680 13.84 - 27.68: 436 27.68 - 41.52: 142 41.52 - 55.36: 27 55.36 - 69.21: 14 Dihedral angle restraints: 6299 sinusoidal: 2548 harmonic: 3751 Sorted by residual: dihedral pdb=" C1' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C5' AMP B1101 " ideal model delta sinusoidal sigma weight residual -123.00 -152.80 29.80 1 8.00e+00 1.56e-02 1.98e+01 dihedral pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" CB PHE A 211 " pdb=" CG PHE A 211 " ideal model delta sinusoidal sigma weight residual -60.00 -0.14 -59.86 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 895 " pdb=" CB ARG A 895 " pdb=" CG ARG A 895 " pdb=" CD ARG A 895 " ideal model delta sinusoidal sigma weight residual -60.00 -118.15 58.15 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 979 0.028 - 0.057: 427 0.057 - 0.085: 98 0.085 - 0.114: 75 0.114 - 0.142: 12 Chirality restraints: 1591 Sorted by residual: chirality pdb=" CA GLN A 385 " pdb=" N GLN A 385 " pdb=" C GLN A 385 " pdb=" CB GLN A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE A 834 " pdb=" N ILE A 834 " pdb=" C ILE A 834 " pdb=" CB ILE A 834 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1588 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 76 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO C 77 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 77 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 77 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 876 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 877 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 877 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 877 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 759 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO A 760 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.014 5.00e-02 4.00e+02 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 2 2.00 - 2.72: 423 2.72 - 3.45: 15082 3.45 - 4.17: 23302 4.17 - 4.90: 42101 Nonbonded interactions: 80910 Sorted by model distance: nonbonded pdb=" NZ LYS C 121 " pdb=" OXT GLY D 157 " model vdw 1.270 2.520 nonbonded pdb=" NZ LYS C 121 " pdb=" C GLY D 157 " model vdw 1.332 3.350 nonbonded pdb=" O GLY A 39 " pdb=" OG1 THR A 125 " model vdw 2.213 2.440 nonbonded pdb=" O ASN A 695 " pdb=" OG SER A 706 " model vdw 2.219 2.440 nonbonded pdb=" OE2 GLU A 592 " pdb=" NH1 ARG B 155 " model vdw 2.233 2.520 ... (remaining 80905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 82 through 157) selection = chain 'D' } 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: 2.410 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: 10.140 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.140 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 : 0.005 0.209 10460 Z= 0.315 Angle : 0.565 13.528 14242 Z= 0.280 Chirality : 0.038 0.142 1591 Planarity : 0.004 0.034 1867 Dihedral : 11.768 69.205 3873 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.00 % Allowed : 7.08 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.54 (0.24), residues: 1291 helix: 1.74 (0.24), residues: 476 sheet: -1.21 (0.38), residues: 185 loop : -0.12 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 95 HIS 0.003 0.001 HIS A 948 PHE 0.007 0.001 PHE A 146 TYR 0.011 0.001 TYR A 603 ARG 0.002 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 1.262 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 171 average time/residue: 0.2346 time to fit residues: 56.6798 Evaluate side-chains 125 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1214 time to fit residues: 5.0748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 41 GLN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 631 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 110 GLN C 43 GLN C 103 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10460 Z= 0.235 Angle : 0.563 6.520 14242 Z= 0.268 Chirality : 0.039 0.144 1591 Planarity : 0.004 0.044 1867 Dihedral : 4.254 43.105 1409 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.91 % Allowed : 10.99 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.53 (0.24), residues: 1291 helix: 1.70 (0.24), residues: 476 sheet: -1.06 (0.38), residues: 193 loop : -0.15 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 614 HIS 0.006 0.001 HIS C 47 PHE 0.009 0.001 PHE A 146 TYR 0.016 0.002 TYR D 96 ARG 0.006 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.152 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 130 average time/residue: 0.2335 time to fit residues: 43.1599 Evaluate side-chains 114 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1049 time to fit residues: 2.9440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 631 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10460 Z= 0.190 Angle : 0.555 7.418 14242 Z= 0.260 Chirality : 0.039 0.164 1591 Planarity : 0.004 0.050 1867 Dihedral : 4.330 43.891 1409 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.91 % Allowed : 12.62 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.51 (0.24), residues: 1291 helix: 1.71 (0.24), residues: 477 sheet: -1.04 (0.38), residues: 185 loop : -0.21 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 614 HIS 0.006 0.001 HIS C 47 PHE 0.009 0.001 PHE A 146 TYR 0.015 0.001 TYR D 96 ARG 0.008 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.090 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 135 average time/residue: 0.2400 time to fit residues: 45.7725 Evaluate side-chains 117 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0993 time to fit residues: 3.4399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.0020 chunk 87 optimal weight: 0.0980 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10460 Z= 0.239 Angle : 0.567 8.200 14242 Z= 0.265 Chirality : 0.040 0.270 1591 Planarity : 0.004 0.045 1867 Dihedral : 4.531 43.976 1409 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.82 % Allowed : 13.90 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.48 (0.24), residues: 1291 helix: 1.67 (0.24), residues: 479 sheet: -1.10 (0.37), residues: 185 loop : -0.21 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 614 HIS 0.005 0.001 HIS C 47 PHE 0.011 0.001 PHE A 146 TYR 0.015 0.001 TYR C 21 ARG 0.008 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 131 average time/residue: 0.2388 time to fit residues: 44.2234 Evaluate side-chains 118 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.313 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0996 time to fit residues: 3.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 0.0050 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10460 Z= 0.210 Angle : 0.550 6.920 14242 Z= 0.258 Chirality : 0.039 0.162 1591 Planarity : 0.004 0.045 1867 Dihedral : 4.516 45.614 1409 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.09 % Allowed : 15.17 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.52 (0.24), residues: 1291 helix: 1.73 (0.24), residues: 480 sheet: -1.10 (0.37), residues: 185 loop : -0.22 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 614 HIS 0.005 0.001 HIS C 47 PHE 0.010 0.001 PHE A 146 TYR 0.011 0.001 TYR C 21 ARG 0.008 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.168 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 120 average time/residue: 0.2303 time to fit residues: 39.9049 Evaluate side-chains 113 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1037 time to fit residues: 3.4565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.0030 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10460 Z= 0.222 Angle : 0.563 7.314 14242 Z= 0.263 Chirality : 0.040 0.308 1591 Planarity : 0.004 0.048 1867 Dihedral : 4.548 47.477 1409 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.91 % Allowed : 15.99 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.49 (0.24), residues: 1291 helix: 1.71 (0.24), residues: 479 sheet: -1.12 (0.37), residues: 185 loop : -0.23 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 614 HIS 0.005 0.001 HIS C 47 PHE 0.011 0.001 PHE A 146 TYR 0.016 0.001 TYR C 21 ARG 0.009 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.076 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 120 average time/residue: 0.2389 time to fit residues: 41.1918 Evaluate side-chains 110 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1000 time to fit residues: 2.3457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN D 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10460 Z= 0.251 Angle : 0.575 7.633 14242 Z= 0.272 Chirality : 0.040 0.171 1591 Planarity : 0.004 0.050 1867 Dihedral : 4.589 50.713 1409 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.54 % Allowed : 17.26 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.44 (0.24), residues: 1291 helix: 1.62 (0.24), residues: 479 sheet: -1.19 (0.37), residues: 185 loop : -0.19 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 614 HIS 0.005 0.001 HIS C 47 PHE 0.017 0.001 PHE D 126 TYR 0.013 0.001 TYR C 21 ARG 0.009 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.201 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 113 average time/residue: 0.2424 time to fit residues: 39.2644 Evaluate side-chains 104 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0946 time to fit residues: 1.8244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.4980 chunk 73 optimal weight: 0.3980 chunk 37 optimal weight: 0.0030 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 112 optimal weight: 0.0570 overall best weight: 0.2508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10460 Z= 0.139 Angle : 0.555 9.541 14242 Z= 0.259 Chirality : 0.039 0.391 1591 Planarity : 0.004 0.049 1867 Dihedral : 4.440 55.095 1409 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.54 % Allowed : 17.71 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.59 (0.24), residues: 1291 helix: 1.75 (0.24), residues: 481 sheet: -1.06 (0.38), residues: 185 loop : -0.13 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 614 HIS 0.005 0.000 HIS C 47 PHE 0.016 0.001 PHE D 126 TYR 0.012 0.001 TYR A1010 ARG 0.015 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 1.203 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 117 average time/residue: 0.2331 time to fit residues: 39.2436 Evaluate side-chains 106 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1000 time to fit residues: 1.8654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 114 optimal weight: 0.0270 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 0.0670 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10460 Z= 0.149 Angle : 0.548 8.216 14242 Z= 0.258 Chirality : 0.038 0.149 1591 Planarity : 0.004 0.048 1867 Dihedral : 4.418 59.014 1409 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.73 % Allowed : 17.53 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.65 (0.24), residues: 1291 helix: 1.83 (0.24), residues: 481 sheet: -1.03 (0.38), residues: 185 loop : -0.13 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 614 HIS 0.004 0.000 HIS C 47 PHE 0.015 0.001 PHE D 126 TYR 0.014 0.001 TYR C 21 ARG 0.010 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.191 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 112 average time/residue: 0.2386 time to fit residues: 38.1512 Evaluate side-chains 109 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0941 time to fit residues: 2.3187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.0060 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10460 Z= 0.198 Angle : 0.569 9.784 14242 Z= 0.267 Chirality : 0.039 0.204 1591 Planarity : 0.004 0.049 1867 Dihedral : 4.405 55.358 1409 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.18 % Allowed : 17.89 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.61 (0.24), residues: 1291 helix: 1.82 (0.24), residues: 479 sheet: -1.09 (0.37), residues: 185 loop : -0.15 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 614 HIS 0.004 0.001 HIS C 47 PHE 0.014 0.001 PHE D 126 TYR 0.013 0.001 TYR C 21 ARG 0.010 0.000 ARG C 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.229 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 111 average time/residue: 0.2477 time to fit residues: 38.8358 Evaluate side-chains 107 residues out of total 1101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 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 = 0.4243 r_free = 0.4243 target = 0.181602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122606 restraints weight = 13703.311| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.27 r_work: 0.3298 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10460 Z= 0.181 Angle : 0.573 10.944 14242 Z= 0.271 Chirality : 0.039 0.190 1591 Planarity : 0.004 0.049 1867 Dihedral : 4.297 47.300 1409 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.36 % Allowed : 17.80 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.61 (0.24), residues: 1291 helix: 1.81 (0.24), residues: 481 sheet: -1.07 (0.38), residues: 185 loop : -0.15 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 614 HIS 0.004 0.001 HIS C 47 PHE 0.009 0.001 PHE A 146 TYR 0.013 0.001 TYR C 21 ARG 0.010 0.000 ARG C 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.32 seconds wall clock time: 42 minutes 28.45 seconds (2548.45 seconds total)