Starting phenix.real_space_refine on Thu Feb 15 08:05:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj4_34832/02_2024/8hj4_34832.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj4_34832/02_2024/8hj4_34832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj4_34832/02_2024/8hj4_34832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj4_34832/02_2024/8hj4_34832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj4_34832/02_2024/8hj4_34832.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj4_34832/02_2024/8hj4_34832.pdb" } resolution = 3.1 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= 0.023 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 113 5.49 5 S 30 5.16 5 C 6932 2.51 5 N 2080 2.21 5 O 2497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 886": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8187 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 43, 'TRANS': 989} Chain breaks: 3 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 9, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2391 Classifications: {'RNA': 113} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 49, 'rna3p_pyr': 56} Link IDs: {'rna2p': 7, 'rna3p': 105} Chain breaks: 1 Chain: "C" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1074 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'TRANS': 129} Time building chain proxies: 6.77, per 1000 atoms: 0.58 Number of scatterers: 11652 At special positions: 0 Unit cell: (113.36, 110.24, 138.32, 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 30 16.00 P 113 15.00 O 2497 8.00 N 2080 7.00 C 6932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.72 Conformation dependent library (CDL) restraints added in 3.1 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 47.0% alpha, 8.9% beta 23 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 57 through 89 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 154 through 172 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.545A pdb=" N LEU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.706A pdb=" N HIS A 201 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 202 " --> pdb=" O TYR A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 230 through 241 removed outlier: 3.980A pdb=" N GLU A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.893A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 298 through 307 removed outlier: 4.231A pdb=" N ASP A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.807A pdb=" N PHE A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.575A pdb=" N ILE A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.127A pdb=" N HIS A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 436 Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 474 through 496 Processing helix chain 'A' and resid 512 through 541 Processing helix chain 'A' and resid 549 through 562 removed outlier: 3.593A pdb=" N ILE A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 4.048A pdb=" N ASN A 579 " --> pdb=" O GLY A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 629 through 641 Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.614A pdb=" N LEU A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 721 through 732 Processing helix chain 'A' and resid 734 through 750 removed outlier: 4.189A pdb=" N MET A 750 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.648A pdb=" N VAL A 821 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 868 removed outlier: 7.008A pdb=" N LYS A 868 " --> pdb=" O THR A 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 865 through 868' Processing helix chain 'A' and resid 869 through 874 removed outlier: 3.816A pdb=" N GLU A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 869 through 874' Processing helix chain 'A' and resid 875 through 879 removed outlier: 3.860A pdb=" N ARG A 878 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU A 879 " --> pdb=" O VAL A 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 875 through 879' Processing helix chain 'A' and resid 881 through 895 removed outlier: 3.785A pdb=" N ARG A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 966 through 971 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'C' and resid 21 through 38 Processing helix chain 'C' and resid 42 through 52 removed outlier: 4.178A pdb=" N GLU C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.625A pdb=" N LYS C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.640A pdb=" N GLU C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.671A pdb=" N PHE C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 502 removed outlier: 7.311A pdb=" N TYR A 11 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N HIS A 502 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU A 13 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 23 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 22 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY A 42 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TRP A 24 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP A 40 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N MET A 26 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU A 38 " --> pdb=" O MET A 26 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU A 28 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N SER A 831 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 43 " --> pdb=" O SER A 831 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 removed outlier: 7.188A pdb=" N LEU A 315 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 587 removed outlier: 3.796A pdb=" N VAL A 606 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 848 through 849 Processing sheet with id=AA6, first strand: chain 'A' and resid 860 through 863 Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908 removed outlier: 4.117A pdb=" N PHE A 907 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 960 through 965 removed outlier: 4.533A pdb=" N PHE A 999 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1046 through 1050 removed outlier: 3.667A pdb=" N GLY A1049 " --> pdb=" O ILE A1030 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A1030 " --> pdb=" O GLY A1049 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN A1031 " --> pdb=" O ALA A1021 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A1005 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A1006 " --> pdb=" O TYR A1061 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.672A pdb=" N LYS C 89 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 15 391 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 8.35 Time building geometry restraints manager: 7.02 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: 3280 1.34 - 1.46: 2661 1.46 - 1.58: 5893 1.58 - 1.70: 224 1.70 - 1.82: 49 Bond restraints: 12107 Sorted by residual: bond pdb=" N VAL A1007 " pdb=" CA VAL A1007 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" N VAL A1009 " pdb=" CA VAL A1009 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.76e+00 bond pdb=" N ILE A 423 " pdb=" CA ILE A 423 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.20e+00 bond pdb=" N VAL A 735 " pdb=" CA VAL A 735 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N LYS A 266 " pdb=" CA LYS A 266 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.22e-02 6.72e+03 7.35e+00 ... (remaining 12102 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.97: 747 105.97 - 112.98: 6576 112.98 - 120.00: 4331 120.00 - 127.01: 4889 127.01 - 134.02: 326 Bond angle restraints: 16869 Sorted by residual: angle pdb=" CA VAL A1007 " pdb=" C VAL A1007 " pdb=" O VAL A1007 " ideal model delta sigma weight residual 121.63 117.61 4.02 9.90e-01 1.02e+00 1.65e+01 angle pdb=" CA GLY A 840 " pdb=" C GLY A 840 " pdb=" O GLY A 840 " ideal model delta sigma weight residual 121.83 117.76 4.07 1.02e+00 9.61e-01 1.59e+01 angle pdb=" N ASN A 526 " pdb=" CA ASN A 526 " pdb=" C ASN A 526 " ideal model delta sigma weight residual 111.82 107.31 4.51 1.16e+00 7.43e-01 1.51e+01 angle pdb=" N GLN A 738 " pdb=" CA GLN A 738 " pdb=" C GLN A 738 " ideal model delta sigma weight residual 111.71 107.28 4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N ILE A 192 " pdb=" CA ILE A 192 " pdb=" C ILE A 192 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 ... (remaining 16864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.17: 6573 20.17 - 40.34: 606 40.34 - 60.52: 212 60.52 - 80.69: 97 80.69 - 100.86: 19 Dihedral angle restraints: 7507 sinusoidal: 4122 harmonic: 3385 Sorted by residual: dihedral pdb=" CA VAL A 91 " pdb=" C VAL A 91 " pdb=" N LEU A 92 " pdb=" CA LEU A 92 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ARG A 402 " pdb=" C ARG A 402 " pdb=" N ILE A 403 " pdb=" CA ILE A 403 " ideal model delta harmonic sigma weight residual 180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP A 683 " pdb=" C ASP A 683 " pdb=" N ARG A 684 " pdb=" CA ARG A 684 " ideal model delta harmonic sigma weight residual 180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 7504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1485 0.038 - 0.076: 323 0.076 - 0.114: 95 0.114 - 0.153: 28 0.153 - 0.191: 13 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA VAL A1007 " pdb=" N VAL A1007 " pdb=" C VAL A1007 " pdb=" CB VAL A1007 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA LYS A 528 " pdb=" N LYS A 528 " pdb=" C LYS A 528 " pdb=" CB LYS A 528 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA LEU A 231 " pdb=" N LEU A 231 " pdb=" C LEU A 231 " pdb=" CB LEU A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 1941 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 772 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.87e+00 pdb=" N PRO A 773 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 773 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 773 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 975 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 955 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C LYS A 955 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS A 955 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY A 956 " -0.011 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1448 2.75 - 3.29: 11677 3.29 - 3.82: 20860 3.82 - 4.36: 24968 4.36 - 4.90: 39166 Nonbonded interactions: 98119 Sorted by model distance: nonbonded pdb=" O ARG A 880 " pdb=" O2' C B 36 " model vdw 2.211 2.440 nonbonded pdb=" NH2 ARG A 138 " pdb=" OP1 U B 21 " model vdw 2.227 2.520 nonbonded pdb=" NE1 TRP A 111 " pdb=" OP1 A B 60 " model vdw 2.250 2.520 nonbonded pdb=" NH1 ARG A 721 " pdb=" OD2 ASP A1036 " model vdw 2.251 2.520 nonbonded pdb=" O ALA A 637 " pdb=" OG1 THR A 641 " model vdw 2.253 2.440 ... (remaining 98114 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.290 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 44.710 Find NCS groups from input model: 0.280 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12107 Z= 0.212 Angle : 0.600 9.577 16869 Z= 0.345 Chirality : 0.040 0.191 1944 Planarity : 0.004 0.049 1776 Dihedral : 18.932 100.859 5315 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.85 % Favored : 92.89 % Rotamer: Outliers : 0.73 % Allowed : 0.62 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1153 helix: 0.24 (0.24), residues: 488 sheet: -1.97 (0.53), residues: 99 loop : -1.37 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.004 0.001 HIS A1024 PHE 0.017 0.001 PHE A 797 TYR 0.009 0.001 TYR C 70 ARG 0.006 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 258 CYS cc_start: 0.5549 (t) cc_final: 0.5306 (t) REVERT: A 728 VAL cc_start: 0.8095 (t) cc_final: 0.7718 (t) REVERT: A 748 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6794 (pttt) REVERT: A 908 TYR cc_start: 0.7215 (m-80) cc_final: 0.6991 (m-80) outliers start: 7 outliers final: 2 residues processed: 113 average time/residue: 0.2783 time to fit residues: 43.6629 Evaluate side-chains 89 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 1012 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN C 101 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12107 Z= 0.183 Angle : 0.586 9.071 16869 Z= 0.298 Chirality : 0.038 0.178 1944 Planarity : 0.004 0.047 1776 Dihedral : 19.485 108.249 3029 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.07 % Favored : 93.76 % Rotamer: Outliers : 1.25 % Allowed : 8.01 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1153 helix: 0.66 (0.24), residues: 493 sheet: -1.77 (0.52), residues: 104 loop : -1.22 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.004 0.001 HIS A 133 PHE 0.020 0.001 PHE C 124 TYR 0.009 0.001 TYR C 41 ARG 0.003 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6648 (pttt) REVERT: A 908 TYR cc_start: 0.7163 (m-80) cc_final: 0.6942 (m-80) REVERT: C 89 LYS cc_start: 0.7337 (tmtt) cc_final: 0.6999 (tmtt) outliers start: 12 outliers final: 6 residues processed: 95 average time/residue: 0.2669 time to fit residues: 35.7246 Evaluate side-chains 85 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1012 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.006 0.063 12107 Z= 0.376 Angle : 0.675 8.728 16869 Z= 0.343 Chirality : 0.043 0.201 1944 Planarity : 0.005 0.053 1776 Dihedral : 19.486 114.155 3026 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.72 % Favored : 92.11 % Rotamer: Outliers : 1.87 % Allowed : 13.22 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1153 helix: 0.48 (0.23), residues: 486 sheet: -2.16 (0.50), residues: 102 loop : -1.42 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 46 HIS 0.005 0.001 HIS A1024 PHE 0.018 0.002 PHE C 124 TYR 0.014 0.002 TYR A 11 ARG 0.004 0.001 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 522 ARG cc_start: 0.7642 (mtp85) cc_final: 0.7418 (mtp85) REVERT: A 706 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7659 (mt) REVERT: A 748 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6710 (pttt) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 0.2885 time to fit residues: 38.3315 Evaluate side-chains 80 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain C residue 88 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12107 Z= 0.256 Angle : 0.599 8.691 16869 Z= 0.306 Chirality : 0.039 0.213 1944 Planarity : 0.004 0.051 1776 Dihedral : 19.438 116.138 3026 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.59 % Favored : 93.24 % Rotamer: Outliers : 2.39 % Allowed : 15.82 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 1153 helix: 0.59 (0.23), residues: 491 sheet: -2.16 (0.49), residues: 104 loop : -1.43 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.004 0.001 HIS A1024 PHE 0.018 0.002 PHE C 124 TYR 0.013 0.001 TYR C 11 ARG 0.002 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6840 (mt) REVERT: A 185 PHE cc_start: 0.2845 (m-10) cc_final: 0.2617 (m-80) REVERT: A 706 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 748 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6744 (pttt) outliers start: 23 outliers final: 15 residues processed: 96 average time/residue: 0.2797 time to fit residues: 37.7104 Evaluate side-chains 92 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12107 Z= 0.168 Angle : 0.553 8.559 16869 Z= 0.282 Chirality : 0.038 0.197 1944 Planarity : 0.004 0.047 1776 Dihedral : 19.385 116.075 3026 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.90 % Favored : 93.93 % Rotamer: Outliers : 2.39 % Allowed : 16.96 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1153 helix: 0.89 (0.23), residues: 493 sheet: -1.65 (0.54), residues: 94 loop : -1.46 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.003 0.001 HIS A 133 PHE 0.020 0.001 PHE C 124 TYR 0.014 0.001 TYR C 70 ARG 0.003 0.000 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.2778 (m-10) cc_final: 0.2561 (m-80) REVERT: A 632 TRP cc_start: 0.6725 (t-100) cc_final: 0.6093 (t-100) REVERT: A 748 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6744 (pttt) REVERT: A 908 TYR cc_start: 0.7121 (m-80) cc_final: 0.6664 (m-80) REVERT: C 50 LEU cc_start: 0.8063 (mt) cc_final: 0.7739 (mt) outliers start: 23 outliers final: 14 residues processed: 102 average time/residue: 0.2723 time to fit residues: 39.4184 Evaluate side-chains 98 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.2980 chunk 110 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12107 Z= 0.308 Angle : 0.624 8.399 16869 Z= 0.318 Chirality : 0.040 0.256 1944 Planarity : 0.005 0.049 1776 Dihedral : 19.380 116.261 3026 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.55 % Favored : 92.28 % Rotamer: Outliers : 2.39 % Allowed : 17.48 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1153 helix: 0.72 (0.23), residues: 494 sheet: -2.33 (0.46), residues: 114 loop : -1.49 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 46 HIS 0.005 0.001 HIS A1024 PHE 0.018 0.002 PHE C 124 TYR 0.013 0.001 TYR A 11 ARG 0.003 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.3044 (m-10) cc_final: 0.2837 (m-80) REVERT: A 706 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 748 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6761 (pttt) REVERT: A 886 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.5448 (mp0) outliers start: 23 outliers final: 15 residues processed: 103 average time/residue: 0.2607 time to fit residues: 37.9368 Evaluate side-chains 98 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12107 Z= 0.193 Angle : 0.567 8.687 16869 Z= 0.288 Chirality : 0.038 0.227 1944 Planarity : 0.004 0.047 1776 Dihedral : 19.363 115.288 3026 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.98 % Favored : 93.84 % Rotamer: Outliers : 2.29 % Allowed : 18.63 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1153 helix: 0.86 (0.23), residues: 500 sheet: -2.02 (0.49), residues: 104 loop : -1.52 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.003 0.001 HIS A 133 PHE 0.021 0.001 PHE C 124 TYR 0.011 0.001 TYR C 11 ARG 0.003 0.000 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.3009 (m-10) cc_final: 0.2793 (m-80) REVERT: A 632 TRP cc_start: 0.6725 (t-100) cc_final: 0.6096 (t-100) REVERT: A 706 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7610 (mt) REVERT: A 748 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6767 (pttt) REVERT: A 886 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.5391 (mp0) REVERT: C 125 TYR cc_start: 0.1895 (OUTLIER) cc_final: 0.1358 (m-80) outliers start: 22 outliers final: 15 residues processed: 103 average time/residue: 0.2825 time to fit residues: 41.0730 Evaluate side-chains 104 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 125 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12107 Z= 0.196 Angle : 0.567 9.026 16869 Z= 0.287 Chirality : 0.038 0.155 1944 Planarity : 0.004 0.046 1776 Dihedral : 19.302 114.713 3026 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 2.08 % Allowed : 18.63 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1153 helix: 0.92 (0.23), residues: 502 sheet: -1.78 (0.53), residues: 94 loop : -1.48 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.003 0.001 HIS A1024 PHE 0.020 0.002 PHE C 124 TYR 0.009 0.001 TYR C 11 ARG 0.003 0.000 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.3218 (m-10) cc_final: 0.2985 (m-80) REVERT: A 552 ASP cc_start: 0.7824 (p0) cc_final: 0.7439 (p0) REVERT: A 632 TRP cc_start: 0.6724 (t-100) cc_final: 0.6109 (t-100) REVERT: A 706 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7606 (mt) REVERT: A 748 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6803 (pttt) REVERT: A 886 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5407 (mp0) REVERT: C 125 TYR cc_start: 0.1893 (OUTLIER) cc_final: 0.1352 (m-80) outliers start: 20 outliers final: 15 residues processed: 107 average time/residue: 0.2743 time to fit residues: 41.9144 Evaluate side-chains 104 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 125 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12107 Z= 0.386 Angle : 0.686 8.980 16869 Z= 0.350 Chirality : 0.042 0.181 1944 Planarity : 0.005 0.050 1776 Dihedral : 19.337 115.224 3026 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.60 % Allowed : 18.31 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1153 helix: 0.59 (0.23), residues: 492 sheet: -2.25 (0.49), residues: 102 loop : -1.63 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 46 HIS 0.006 0.001 HIS A1024 PHE 0.023 0.002 PHE A 537 TYR 0.017 0.002 TYR C 11 ARG 0.003 0.000 ARG A 880 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 ASP cc_start: 0.7830 (p0) cc_final: 0.7417 (p0) REVERT: A 706 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7680 (mt) REVERT: A 748 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.6884 (pttt) REVERT: A 886 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.5539 (mp0) REVERT: C 72 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7356 (t0) REVERT: C 125 TYR cc_start: 0.2081 (OUTLIER) cc_final: 0.1544 (m-10) outliers start: 25 outliers final: 17 residues processed: 103 average time/residue: 0.2669 time to fit residues: 38.9346 Evaluate side-chains 101 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 125 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.0470 chunk 120 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 100 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12107 Z= 0.150 Angle : 0.568 9.487 16869 Z= 0.289 Chirality : 0.037 0.155 1944 Planarity : 0.004 0.046 1776 Dihedral : 19.238 113.765 3026 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.08 % Allowed : 18.83 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1153 helix: 0.94 (0.24), residues: 504 sheet: -2.23 (0.46), residues: 117 loop : -1.43 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 127 HIS 0.010 0.001 HIS A 201 PHE 0.023 0.001 PHE C 124 TYR 0.010 0.001 TYR C 11 ARG 0.004 0.000 ARG A 916 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 ASP cc_start: 0.7782 (p0) cc_final: 0.7430 (p0) REVERT: A 632 TRP cc_start: 0.6700 (t-100) cc_final: 0.6185 (t-100) REVERT: A 706 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7570 (mt) REVERT: A 748 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.6886 (pttt) REVERT: A 886 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.5412 (mp0) REVERT: C 125 TYR cc_start: 0.1932 (OUTLIER) cc_final: 0.1374 (m-80) outliers start: 20 outliers final: 13 residues processed: 109 average time/residue: 0.2667 time to fit residues: 41.2439 Evaluate side-chains 101 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 125 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.0470 chunk 42 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.182619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.143964 restraints weight = 18479.575| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.02 r_work: 0.4017 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12107 Z= 0.166 Angle : 0.565 9.489 16869 Z= 0.286 Chirality : 0.036 0.154 1944 Planarity : 0.004 0.046 1776 Dihedral : 19.139 113.437 3026 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.08 % Allowed : 18.94 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1153 helix: 1.10 (0.24), residues: 500 sheet: -2.16 (0.47), residues: 112 loop : -1.41 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.011 0.001 HIS A 201 PHE 0.023 0.001 PHE C 124 TYR 0.008 0.001 TYR A 908 ARG 0.005 0.000 ARG A 916 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.21 seconds wall clock time: 42 minutes 20.25 seconds (2540.25 seconds total)