Starting phenix.real_space_refine on Fri Jul 19 12:25:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/07_2024/8ien_35387_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/07_2024/8ien_35387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/07_2024/8ien_35387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/07_2024/8ien_35387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/07_2024/8ien_35387_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/07_2024/8ien_35387_neut_trim.cif" } resolution = 3.25 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= 0.003 sd= 0.075 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 4959 2.51 5 N 1320 2.21 5 O 1340 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 235": "OE1" <-> "OE2" Residue "P GLU 303": "OE1" <-> "OE2" Residue "P GLU 348": "OE1" <-> "OE2" Residue "P GLU 367": "OE1" <-> "OE2" Residue "P GLU 520": "OE1" <-> "OE2" Residue "P GLU 616": "OE1" <-> "OE2" Residue "P GLU 782": "OE1" <-> "OE2" Residue "P GLU 861": "OE1" <-> "OE2" Residue "P GLU 1135": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7678 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 7644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7644 Classifications: {'peptide': 991} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 65, 'TRANS': 922} Chain breaks: 6 Chain: "P" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.30, per 1000 atoms: 0.69 Number of scatterers: 7678 At special positions: 0 Unit cell: (86.505, 112.785, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1340 8.00 N 1320 7.00 C 4959 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 48.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'P' and resid 50 through 59 Processing helix chain 'P' and resid 61 through 66 Processing helix chain 'P' and resid 69 through 77 removed outlier: 3.828A pdb=" N ARG P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 201 Processing helix chain 'P' and resid 208 through 217 removed outlier: 3.652A pdb=" N ARG P 212 " --> pdb=" O ASP P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 236 Processing helix chain 'P' and resid 238 through 254 Processing helix chain 'P' and resid 256 through 290 Processing helix chain 'P' and resid 310 through 312 No H-bonds generated for 'chain 'P' and resid 310 through 312' Processing helix chain 'P' and resid 403 through 413 removed outlier: 4.003A pdb=" N VAL P 408 " --> pdb=" O LYS P 404 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS P 413 " --> pdb=" O SER P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 427 through 451 removed outlier: 3.719A pdb=" N ILE P 444 " --> pdb=" O THR P 440 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG P 449 " --> pdb=" O PHE P 445 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG P 451 " --> pdb=" O LEU P 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 469 removed outlier: 3.582A pdb=" N ARG P 460 " --> pdb=" O GLU P 456 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU P 462 " --> pdb=" O VAL P 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL P 469 " --> pdb=" O VAL P 465 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 492 removed outlier: 4.347A pdb=" N CYS P 480 " --> pdb=" O ALA P 476 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR P 481 " --> pdb=" O MET P 477 " (cutoff:3.500A) Processing helix chain 'P' and resid 498 through 504 removed outlier: 4.416A pdb=" N ASN P 502 " --> pdb=" O PRO P 498 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU P 503 " --> pdb=" O LEU P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 549 through 558 Processing helix chain 'P' and resid 571 through 581 Processing helix chain 'P' and resid 656 through 664 removed outlier: 3.583A pdb=" N VAL P 660 " --> pdb=" O SER P 656 " (cutoff:3.500A) Processing helix chain 'P' and resid 673 through 683 removed outlier: 3.614A pdb=" N LEU P 677 " --> pdb=" O PHE P 673 " (cutoff:3.500A) Processing helix chain 'P' and resid 731 through 742 removed outlier: 3.754A pdb=" N VAL P 735 " --> pdb=" O GLN P 731 " (cutoff:3.500A) Processing helix chain 'P' and resid 753 through 765 removed outlier: 3.520A pdb=" N ALA P 757 " --> pdb=" O ASN P 753 " (cutoff:3.500A) Processing helix chain 'P' and resid 826 through 835 Processing helix chain 'P' and resid 840 through 847 Processing helix chain 'P' and resid 855 through 868 Processing helix chain 'P' and resid 882 through 889 Processing helix chain 'P' and resid 914 through 955 removed outlier: 4.249A pdb=" N MET P 918 " --> pdb=" O GLU P 914 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 970 Processing helix chain 'P' and resid 970 through 978 Processing helix chain 'P' and resid 998 through 1026 removed outlier: 3.750A pdb=" N LEU P1017 " --> pdb=" O THR P1013 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY P1018 " --> pdb=" O GLY P1014 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY P1019 " --> pdb=" O VAL P1015 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR P1020 " --> pdb=" O GLN P1016 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA P1025 " --> pdb=" O PHE P1021 " (cutoff:3.500A) Processing helix chain 'P' and resid 1037 through 1041 removed outlier: 3.651A pdb=" N ASN P1041 " --> pdb=" O ALA P1038 " (cutoff:3.500A) Processing helix chain 'P' and resid 1044 through 1065 removed outlier: 3.776A pdb=" N THR P1048 " --> pdb=" O ASN P1044 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) Processing helix chain 'P' and resid 1078 through 1098 Processing helix chain 'P' and resid 1113 through 1139 Processing helix chain 'P' and resid 1141 through 1146 Processing helix chain 'P' and resid 1156 through 1169 Processing sheet with id=AA1, first strand: chain 'P' and resid 40 through 41 removed outlier: 4.136A pdb=" N CYS P 41 " --> pdb=" O ILE P 90 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE P 90 " --> pdb=" O CYS P 41 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE P 103 " --> pdb=" O LEU P 167 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU P 167 " --> pdb=" O PHE P 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR P 166 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE P 174 " --> pdb=" O TYR P 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR P 183 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 303 through 308 removed outlier: 3.843A pdb=" N GLU P 303 " --> pdb=" O ARG P 299 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS P 296 " --> pdb=" O VAL P 319 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N CYS P 317 " --> pdb=" O CYS P 298 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU P 392 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR P 396 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASP P 330 " --> pdb=" O THR P 396 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA P 331 " --> pdb=" O LEU P 374 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU P 374 " --> pdb=" O ALA P 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 351 through 354 removed outlier: 3.770A pdb=" N VAL P 340 " --> pdb=" O VAL P 352 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS P 354 " --> pdb=" O CYS P 338 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN P 341 " --> pdb=" O ILE P 380 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE P 380 " --> pdb=" O ASN P 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 493 through 495 removed outlier: 5.895A pdb=" N GLY P 892 " --> pdb=" O PHE P 906 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER P 908 " --> pdb=" O GLY P 892 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER P 894 " --> pdb=" O SER P 908 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL P 873 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ILE P 893 " --> pdb=" O VAL P 873 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET P 875 " --> pdb=" O ILE P 893 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU P 509 " --> pdb=" O GLY P 874 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N CYS P 876 " --> pdb=" O LEU P 509 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS P 511 " --> pdb=" O CYS P 876 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR P 849 " --> pdb=" O ALA P 746 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU P 823 " --> pdb=" O GLY P 848 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS P 772 " --> pdb=" O ALA P 824 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER P 788 " --> pdb=" O LEU P 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 624 through 627 removed outlier: 4.350A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL P 640 " --> pdb=" O HIS P 626 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL P 641 " --> pdb=" O GLU P 650 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU P 650 " --> pdb=" O VAL P 641 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY P 655 " --> pdb=" O ALA P 689 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA P 689 " --> pdb=" O GLY P 655 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY P 720 " --> pdb=" O LEU P 690 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER P 692 " --> pdb=" O LEU P 718 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU P 718 " --> pdb=" O SER P 692 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1071 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: 2.46 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2449 1.35 - 1.46: 1687 1.46 - 1.58: 3623 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 7842 Sorted by residual: bond pdb=" C11 SPM P1204 " pdb=" C12 SPM P1204 " ideal model delta sigma weight residual 1.527 1.395 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C12 SPM P1204 " pdb=" C13 SPM P1204 " ideal model delta sigma weight residual 1.527 1.407 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 7837 not shown) Histogram of bond angle deviations from ideal: 89.99 - 107.99: 391 107.99 - 125.99: 10137 125.99 - 143.99: 139 143.99 - 162.00: 0 162.00 - 180.00: 2 Bond angle restraints: 10669 Sorted by residual: angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F2 ALF P1202 " ideal model delta sigma weight residual 108.68 179.98 -71.30 3.00e+00 1.11e-01 5.65e+02 angle pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 109.63 180.00 -70.37 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.69 90.01 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.59 90.01 19.58 3.00e+00 1.11e-01 4.26e+01 ... (remaining 10664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4247 17.68 - 35.35: 401 35.35 - 53.03: 71 53.03 - 70.70: 16 70.70 - 88.38: 5 Dihedral angle restraints: 4740 sinusoidal: 1880 harmonic: 2860 Sorted by residual: dihedral pdb=" CA ASP P 189 " pdb=" CB ASP P 189 " pdb=" CG ASP P 189 " pdb=" OD1 ASP P 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.84 56.84 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU P 650 " pdb=" CG GLU P 650 " pdb=" CD GLU P 650 " pdb=" OE1 GLU P 650 " ideal model delta sinusoidal sigma weight residual 0.00 88.38 -88.38 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LEU P 968 " pdb=" C LEU P 968 " pdb=" N VAL P 969 " pdb=" CA VAL P 969 " ideal model delta harmonic sigma weight residual 180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 4737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 996 0.044 - 0.088: 197 0.088 - 0.132: 69 0.132 - 0.176: 2 0.176 - 0.220: 2 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA SER P 425 " pdb=" N SER P 425 " pdb=" C SER P 425 " pdb=" CB SER P 425 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS P 424 " pdb=" N HIS P 424 " pdb=" C HIS P 424 " pdb=" CB HIS P 424 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA PRO P 618 " pdb=" N PRO P 618 " pdb=" C PRO P 618 " pdb=" CB PRO P 618 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 1263 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO P 618 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO P 619 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO P 619 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 619 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET P 426 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET P 426 " -0.030 2.00e-02 2.50e+03 pdb=" O MET P 426 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS P 427 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU P1042 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO P1043 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO P1043 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P1043 " -0.019 5.00e-02 4.00e+02 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 215 2.71 - 3.26: 7394 3.26 - 3.81: 11972 3.81 - 4.35: 14110 4.35 - 4.90: 24051 Nonbonded interactions: 57742 Sorted by model distance: nonbonded pdb="MG MG P1201 " pdb=" F1 ALF P1202 " model vdw 2.168 2.120 nonbonded pdb=" CG2 VAL P 467 " pdb=" C12 SPM P1204 " model vdw 2.241 3.860 nonbonded pdb=" OD2 ASP P 513 " pdb="MG MG P1201 " model vdw 2.252 2.170 nonbonded pdb=" O THR P 515 " pdb="MG MG P1201 " model vdw 2.280 2.170 nonbonded pdb=" CZ3 TRP P 251 " pdb=" C9 SPM P1204 " model vdw 2.282 3.740 ... (remaining 57737 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: 1.210 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.200 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0170 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 : 0.004 0.132 7842 Z= 0.243 Angle : 1.211 71.295 10669 Z= 0.486 Chirality : 0.040 0.220 1266 Planarity : 0.004 0.050 1339 Dihedral : 14.043 88.379 2894 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 0.24 % Allowed : 2.49 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.25), residues: 977 helix: -0.46 (0.23), residues: 450 sheet: -1.34 (0.62), residues: 61 loop : -2.50 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 67 HIS 0.002 0.000 HIS P 190 PHE 0.015 0.001 PHE P1128 TYR 0.015 0.001 TYR P 256 ARG 0.002 0.000 ARG P1148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2877 (mt) cc_final: 0.2586 (pt) REVERT: P 326 LEU cc_start: 0.3219 (tp) cc_final: 0.2997 (pp) REVERT: P 526 MET cc_start: -0.0095 (pmm) cc_final: -0.1444 (tpp) REVERT: P 577 MET cc_start: 0.1892 (mtp) cc_final: 0.0826 (tmm) REVERT: P 637 MET cc_start: 0.1190 (tmm) cc_final: 0.0942 (mtp) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.1869 time to fit residues: 22.6769 Evaluate side-chains 55 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 HIS ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 281 GLN P 559 HIS ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN P 962 GLN P1127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0792 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7842 Z= 0.229 Angle : 0.938 33.677 10669 Z= 0.392 Chirality : 0.042 0.149 1266 Planarity : 0.005 0.046 1339 Dihedral : 5.687 55.652 1095 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.59 % Allowed : 9.35 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.30 (0.26), residues: 977 helix: 0.31 (0.24), residues: 450 sheet: -0.65 (0.59), residues: 76 loop : -2.18 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 251 HIS 0.004 0.001 HIS P 822 PHE 0.011 0.002 PHE P 906 TYR 0.024 0.002 TYR P 483 ARG 0.005 0.000 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2946 (mt) cc_final: 0.2571 (pt) REVERT: P 288 MET cc_start: -0.1032 (ptt) cc_final: -0.1641 (tpp) REVERT: P 326 LEU cc_start: 0.4306 (tp) cc_final: 0.2418 (mp) REVERT: P 526 MET cc_start: -0.0412 (pmm) cc_final: -0.2374 (tpt) REVERT: P 577 MET cc_start: 0.2250 (mtp) cc_final: 0.0684 (tmm) REVERT: P 637 MET cc_start: 0.0741 (tmm) cc_final: 0.0380 (mtp) REVERT: P 978 MET cc_start: 0.2377 (mtt) cc_final: 0.1403 (mmm) outliers start: 5 outliers final: 4 residues processed: 66 average time/residue: 0.1567 time to fit residues: 16.4655 Evaluate side-chains 60 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 50 TYR Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 944 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 219 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0915 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7842 Z= 0.163 Angle : 0.864 29.917 10669 Z= 0.347 Chirality : 0.040 0.146 1266 Planarity : 0.004 0.044 1339 Dihedral : 5.244 57.902 1095 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.36 % Allowed : 12.78 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.80 (0.27), residues: 977 helix: 0.85 (0.25), residues: 454 sheet: -0.41 (0.58), residues: 76 loop : -2.09 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 67 HIS 0.002 0.001 HIS P 84 PHE 0.010 0.001 PHE P1128 TYR 0.021 0.001 TYR P 483 ARG 0.004 0.000 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2915 (mt) cc_final: 0.2601 (pt) REVERT: P 288 MET cc_start: -0.1359 (ptt) cc_final: -0.1676 (tpp) REVERT: P 326 LEU cc_start: 0.4725 (tp) cc_final: 0.3146 (pp) REVERT: P 573 MET cc_start: 0.2193 (ptt) cc_final: 0.1688 (ptt) REVERT: P 577 MET cc_start: 0.2457 (mtp) cc_final: 0.0599 (tmm) REVERT: P 978 MET cc_start: 0.1853 (mtt) cc_final: 0.1534 (mmm) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.1484 time to fit residues: 13.7960 Evaluate side-chains 57 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 85 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 81 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1047 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1289 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7842 Z= 0.209 Angle : 0.891 30.187 10669 Z= 0.368 Chirality : 0.041 0.161 1266 Planarity : 0.005 0.049 1339 Dihedral : 5.383 56.445 1095 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.01 % Allowed : 13.61 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.27), residues: 977 helix: 0.87 (0.25), residues: 454 sheet: 0.04 (0.56), residues: 74 loop : -2.03 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P1028 HIS 0.002 0.001 HIS P 390 PHE 0.013 0.001 PHE P 906 TYR 0.020 0.002 TYR P 256 ARG 0.005 0.000 ARG P 853 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2779 (mt) cc_final: 0.2576 (pt) REVERT: P 288 MET cc_start: -0.1128 (ptt) cc_final: -0.1581 (tpp) REVERT: P 459 ILE cc_start: 0.0787 (OUTLIER) cc_final: 0.0474 (pt) REVERT: P 483 TYR cc_start: 0.2368 (m-80) cc_final: 0.0420 (m-10) REVERT: P 526 MET cc_start: 0.0595 (mpp) cc_final: -0.2492 (tpt) REVERT: P 577 MET cc_start: 0.2687 (mtp) cc_final: 0.0949 (tmm) REVERT: P 748 MET cc_start: 0.3046 (tmm) cc_final: 0.2809 (ptm) REVERT: P 964 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6388 (tp) outliers start: 17 outliers final: 5 residues processed: 80 average time/residue: 0.1630 time to fit residues: 19.5746 Evaluate side-chains 66 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 962 GLN Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.0070 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 HIS ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN P 847 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1860 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7842 Z= 0.240 Angle : 0.979 30.805 10669 Z= 0.419 Chirality : 0.046 0.224 1266 Planarity : 0.006 0.076 1339 Dihedral : 5.510 57.503 1095 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.01 % Allowed : 17.87 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.19 (0.26), residues: 977 helix: 0.42 (0.24), residues: 458 sheet: -0.03 (0.59), residues: 67 loop : -2.27 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P1028 HIS 0.005 0.001 HIS P 497 PHE 0.027 0.002 PHE P1051 TYR 0.031 0.003 TYR P 871 ARG 0.012 0.001 ARG P 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: P 459 ILE cc_start: 0.1454 (OUTLIER) cc_final: 0.0915 (mm) REVERT: P 577 MET cc_start: 0.2930 (mtp) cc_final: 0.1022 (tmm) REVERT: P 837 PHE cc_start: 0.5524 (t80) cc_final: 0.4730 (m-10) REVERT: P 1091 VAL cc_start: 0.3232 (p) cc_final: 0.2964 (t) outliers start: 17 outliers final: 8 residues processed: 91 average time/residue: 0.1564 time to fit residues: 21.0408 Evaluate side-chains 75 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 573 MET Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 962 GLN Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.0870 chunk 86 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2115 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7842 Z= 0.234 Angle : 0.970 30.924 10669 Z= 0.416 Chirality : 0.045 0.282 1266 Planarity : 0.006 0.051 1339 Dihedral : 5.365 59.248 1095 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.72 % Allowed : 18.34 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.16 (0.26), residues: 977 helix: 0.48 (0.24), residues: 458 sheet: 0.19 (0.72), residues: 51 loop : -2.24 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P1028 HIS 0.019 0.001 HIS P 198 PHE 0.025 0.002 PHE P1051 TYR 0.033 0.003 TYR P 871 ARG 0.010 0.001 ARG P 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: P 327 MET cc_start: 0.2146 (mmm) cc_final: 0.1386 (mmm) outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 0.1390 time to fit residues: 19.8399 Evaluate side-chains 86 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 573 MET Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 659 LEU Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 962 GLN Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1021 PHE Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1044 ASN Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.0070 chunk 44 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2104 moved from start: 0.7985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7842 Z= 0.181 Angle : 0.911 29.941 10669 Z= 0.377 Chirality : 0.042 0.181 1266 Planarity : 0.005 0.050 1339 Dihedral : 4.940 56.485 1095 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.13 % Allowed : 19.76 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 977 helix: 0.92 (0.24), residues: 459 sheet: -0.06 (0.64), residues: 66 loop : -2.12 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P1028 HIS 0.005 0.001 HIS P 198 PHE 0.015 0.001 PHE P 931 TYR 0.020 0.002 TYR P 871 ARG 0.003 0.000 ARG P 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 327 MET cc_start: 0.2311 (mmm) cc_final: 0.1878 (mmt) REVERT: P 380 ILE cc_start: 0.4131 (mp) cc_final: 0.3807 (mp) REVERT: P 577 MET cc_start: 0.3506 (mtp) cc_final: 0.0768 (tmm) REVERT: P 676 MET cc_start: -0.0265 (ttm) cc_final: -0.0514 (tpp) REVERT: P 962 GLN cc_start: 0.2974 (OUTLIER) cc_final: 0.2735 (mp10) outliers start: 18 outliers final: 12 residues processed: 85 average time/residue: 0.1311 time to fit residues: 17.7486 Evaluate side-chains 80 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 937 MET Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 962 GLN Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2205 moved from start: 0.8557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7842 Z= 0.178 Angle : 0.901 30.019 10669 Z= 0.369 Chirality : 0.041 0.194 1266 Planarity : 0.005 0.052 1339 Dihedral : 4.770 57.644 1095 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.37 % Allowed : 20.83 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.47 (0.27), residues: 977 helix: 1.15 (0.24), residues: 459 sheet: -0.14 (0.65), residues: 65 loop : -1.97 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 643 HIS 0.005 0.001 HIS P 198 PHE 0.009 0.001 PHE P 963 TYR 0.019 0.002 TYR P 871 ARG 0.003 0.000 ARG P 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: P 257 TYR cc_start: 0.1310 (OUTLIER) cc_final: -0.1638 (m-80) REVERT: P 339 MET cc_start: 0.2082 (ptp) cc_final: 0.1717 (ptt) REVERT: P 1045 TYR cc_start: 0.1288 (m-80) cc_final: 0.0457 (m-80) outliers start: 20 outliers final: 13 residues processed: 89 average time/residue: 0.1406 time to fit residues: 19.5800 Evaluate side-chains 81 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 526 MET Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 58 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 675 GLN P 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2435 moved from start: 0.9510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7842 Z= 0.203 Angle : 0.956 30.853 10669 Z= 0.404 Chirality : 0.043 0.176 1266 Planarity : 0.005 0.051 1339 Dihedral : 5.158 58.594 1095 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.25 % Allowed : 21.18 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.77 (0.27), residues: 977 helix: 0.85 (0.24), residues: 466 sheet: -0.21 (0.66), residues: 65 loop : -2.13 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P1028 HIS 0.006 0.001 HIS P 198 PHE 0.009 0.001 PHE P 512 TYR 0.033 0.002 TYR P 680 ARG 0.004 0.000 ARG P 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: P 257 TYR cc_start: 0.1667 (OUTLIER) cc_final: -0.1431 (m-80) REVERT: P 339 MET cc_start: 0.2043 (ptp) cc_final: 0.1704 (ptt) REVERT: P 940 TYR cc_start: 0.4283 (OUTLIER) cc_final: 0.2388 (t80) REVERT: P 1009 MET cc_start: 0.5307 (mmt) cc_final: 0.5074 (mmt) REVERT: P 1045 TYR cc_start: 0.1239 (m-80) cc_final: -0.0017 (m-80) REVERT: P 1046 GLU cc_start: 0.4162 (mp0) cc_final: 0.3918 (mp0) outliers start: 19 outliers final: 15 residues processed: 88 average time/residue: 0.1318 time to fit residues: 18.1734 Evaluate side-chains 85 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 528 VAL Chi-restraints excluded: chain P residue 675 GLN Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 937 MET Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1050 VAL Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 455 ASN ** P 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1047 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2584 moved from start: 1.0182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7842 Z= 0.225 Angle : 0.979 30.809 10669 Z= 0.417 Chirality : 0.044 0.200 1266 Planarity : 0.005 0.051 1339 Dihedral : 5.410 59.485 1095 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.89 % Allowed : 22.60 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 977 helix: 0.74 (0.24), residues: 466 sheet: -0.24 (0.66), residues: 65 loop : -2.28 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 175 HIS 0.007 0.001 HIS P 198 PHE 0.038 0.002 PHE P1116 TYR 0.024 0.002 TYR P 871 ARG 0.003 0.000 ARG P 924 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 257 TYR cc_start: 0.1893 (OUTLIER) cc_final: -0.1219 (m-80) REVERT: P 339 MET cc_start: 0.2103 (ptp) cc_final: 0.1759 (ptt) REVERT: P 373 THR cc_start: 0.0565 (OUTLIER) cc_final: -0.0362 (m) REVERT: P 451 ARG cc_start: 0.2447 (tpt90) cc_final: 0.1925 (mmm160) REVERT: P 676 MET cc_start: 0.1115 (ttm) cc_final: 0.0246 (tpp) REVERT: P 940 TYR cc_start: 0.4160 (OUTLIER) cc_final: 0.2353 (t80) REVERT: P 1009 MET cc_start: 0.5546 (mmt) cc_final: 0.5291 (mmt) REVERT: P 1045 TYR cc_start: 0.1814 (m-80) cc_final: 0.0394 (m-80) REVERT: P 1046 GLU cc_start: 0.4354 (mp0) cc_final: 0.4115 (mp0) REVERT: P 1119 LEU cc_start: 0.2902 (tt) cc_final: 0.2503 (tp) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.1513 time to fit residues: 20.5867 Evaluate side-chains 86 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 575 LEU Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1050 VAL Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 56 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 455 ASN P 675 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.283175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.270447 restraints weight = 12727.072| |-----------------------------------------------------------------------------| r_work (start): 0.5000 rms_B_bonded: 1.62 r_work: 0.4939 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4856 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2794 moved from start: 1.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7842 Z= 0.205 Angle : 0.965 31.106 10669 Z= 0.409 Chirality : 0.043 0.191 1266 Planarity : 0.005 0.051 1339 Dihedral : 5.503 57.624 1095 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.25 % Allowed : 23.08 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.05 (0.27), residues: 977 helix: 0.73 (0.24), residues: 463 sheet: -0.26 (0.65), residues: 66 loop : -2.40 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP P 175 HIS 0.007 0.001 HIS P 198 PHE 0.031 0.002 PHE P1116 TYR 0.021 0.002 TYR P 871 ARG 0.003 0.000 ARG P 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1889.11 seconds wall clock time: 34 minutes 29.09 seconds (2069.09 seconds total)