Starting phenix.real_space_refine on Wed Jul 30 05:46:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nl2_49515/07_2025/9nl2_49515.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nl2_49515/07_2025/9nl2_49515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nl2_49515/07_2025/9nl2_49515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nl2_49515/07_2025/9nl2_49515.map" model { file = "/net/cci-nas-00/data/ceres_data/9nl2_49515/07_2025/9nl2_49515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nl2_49515/07_2025/9nl2_49515.cif" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 121 atoms to isotropic. 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 Zn 4 6.06 5 P 159 5.49 5 Mg 1 5.21 5 S 50 5.16 5 C 7134 2.51 5 N 2172 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8854 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1049} Chain breaks: 1 Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "P" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1140 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 24, 'rna3p_pyr': 18} Link IDs: {'rna2p': 11, 'rna3p': 41} Chain breaks: 2 Chain: "T" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1052 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 1, ' ZN': 4, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 107 SG CYS A 14 79.077 95.346 69.639 1.00 95.68 S ATOM 131 SG CYS A 17 82.012 97.787 70.031 1.00101.52 S ATOM 340 SG CYS A 44 60.507 92.311 61.054 1.00 92.73 S ATOM 360 SG CYS A 47 57.484 89.668 62.141 1.00101.78 S ATOM 489 SG CYS A 64 57.087 92.335 59.338 1.00 99.79 S ATOM 594 SG CYS A 78 47.731 69.980 70.976 1.00 86.36 S ATOM 616 SG CYS A 81 50.695 72.437 70.309 1.00 87.31 S ATOM 7380 SG CYS A 941 93.349 100.820 36.648 1.00 91.42 S ATOM 7405 SG CYS A 944 95.312 102.733 33.786 1.00 83.84 S ATOM 7509 SG CYS A 958 96.971 100.002 35.868 1.00 91.83 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' TTP A1206 " occ=0.65 ... (27 atoms not shown) pdb=" PG TTP A1206 " occ=0.65 Time building chain proxies: 7.23, per 1000 atoms: 0.60 Number of scatterers: 12138 At special positions: 0 Unit cell: (133.096, 119.472, 100.608, 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) Zn 4 29.99 S 50 16.00 P 159 15.00 Mg 1 11.99 O 2618 8.00 N 2172 7.00 C 7134 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 35 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 30 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 17 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 14 " pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 60 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 64 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 44 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 47 " pdb=" ZN A1204 " pdb="ZN ZN A1204 " - pdb=" NE2 HIS A 99 " pdb="ZN ZN A1204 " - pdb=" NE2 HIS A 94 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 81 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 78 " pdb=" ZN A1205 " pdb="ZN ZN A1205 " - pdb=" NE2 HIS A 953 " pdb="ZN ZN A1205 " - pdb=" SG CYS A 958 " pdb="ZN ZN A1205 " - pdb=" SG CYS A 941 " pdb="ZN ZN A1205 " - pdb=" SG CYS A 944 " Number of angles added : 10 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 55.0% alpha, 5.7% beta 55 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.737A pdb=" N ILE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 127 through 141 Processing helix chain 'A' and resid 149 through 155 removed outlier: 4.226A pdb=" N ASP A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.628A pdb=" N THR A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 239 through 256 Processing helix chain 'A' and resid 284 through 301 Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.563A pdb=" N ALA A 356 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 372 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 429 through 435 removed outlier: 4.211A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 464 Processing helix chain 'A' and resid 477 through 497 removed outlier: 3.736A pdb=" N GLU A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 568 through 588 removed outlier: 4.600A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) Proline residue: A 580 - end of helix Processing helix chain 'A' and resid 614 through 633 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 694 through 708 Processing helix chain 'A' and resid 712 through 724 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.737A pdb=" N ILE A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 758 Processing helix chain 'A' and resid 764 through 770 removed outlier: 3.575A pdb=" N ILE A 768 " --> pdb=" O CYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 781 through 799 Proline residue: A 787 - end of helix Processing helix chain 'A' and resid 802 through 812 removed outlier: 3.618A pdb=" N ASN A 812 " --> pdb=" O ILE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 825 removed outlier: 3.751A pdb=" N GLU A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.581A pdb=" N LEU A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 882 removed outlier: 3.617A pdb=" N LEU A 882 " --> pdb=" O HIS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 904 removed outlier: 4.074A pdb=" N GLN A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 950 through 957 Processing helix chain 'A' and resid 958 through 960 No H-bonds generated for 'chain 'A' and resid 958 through 960' Processing helix chain 'A' and resid 961 through 983 Processing helix chain 'A' and resid 1026 through 1038 removed outlier: 4.546A pdb=" N GLU A1030 " --> pdb=" O GLU A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1043 through 1052 Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.940A pdb=" N GLU A1074 " --> pdb=" O PRO A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1120 removed outlier: 4.984A pdb=" N GLY A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A1114 " --> pdb=" O GLU A1110 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN A1116 " --> pdb=" O ILE A1112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 425 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 604 removed outlier: 3.519A pdb=" N GLY A 643 " --> pdb=" O ASN A 669 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 508 removed outlier: 4.479A pdb=" N LYS A 635 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 548 through 549 Processing sheet with id=AA7, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AA8, first strand: chain 'A' and resid 841 through 842 Processing sheet with id=AA9, first strand: chain 'A' and resid 986 through 989 Processing sheet with id=AB1, first strand: chain 'A' and resid 1018 through 1021 removed outlier: 6.450A pdb=" N THR A1019 " --> pdb=" O LEU A1063 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 438 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 6.17 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2628 1.33 - 1.45: 3408 1.45 - 1.57: 6290 1.57 - 1.70: 311 1.70 - 1.82: 73 Bond restraints: 12710 Sorted by residual: bond pdb=" N GLN A 1 " pdb=" CA GLN A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" CB MET A 157 " pdb=" CG MET A 157 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.34e+00 bond pdb=" C1' DC B 24 " pdb=" N1 DC B 24 " ideal model delta sigma weight residual 1.490 1.536 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" N1 DC B 61 " pdb=" C2 DC B 61 " ideal model delta sigma weight residual 1.399 1.370 0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1' DC T 11 " pdb=" N1 DC T 11 " ideal model delta sigma weight residual 1.490 1.533 -0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 12705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.30: 17878 8.30 - 16.61: 2 16.61 - 24.91: 2 24.91 - 33.22: 4 33.22 - 41.52: 1 Bond angle restraints: 17887 Sorted by residual: angle pdb=" OP1 DC B 57 " pdb=" P DC B 57 " pdb=" OP2 DC B 57 " ideal model delta sigma weight residual 120.00 78.48 41.52 3.00e+00 1.11e-01 1.92e+02 angle pdb=" O3' DA B 56 " pdb=" P DC B 57 " pdb=" OP1 DC B 57 " ideal model delta sigma weight residual 108.00 76.01 31.99 3.00e+00 1.11e-01 1.14e+02 angle pdb=" OP2 DC B 57 " pdb=" P DC B 57 " pdb=" O5' DC B 57 " ideal model delta sigma weight residual 108.00 76.63 31.37 3.00e+00 1.11e-01 1.09e+02 angle pdb=" O3' DA B 56 " pdb=" P DC B 57 " pdb=" OP2 DC B 57 " ideal model delta sigma weight residual 108.00 139.35 -31.35 3.00e+00 1.11e-01 1.09e+02 angle pdb=" O3' DA B 28 " pdb=" P DA B 29 " pdb=" OP1 DA B 29 " ideal model delta sigma weight residual 108.00 80.96 27.04 3.00e+00 1.11e-01 8.13e+01 ... (remaining 17882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 6678 33.71 - 67.41: 770 67.41 - 101.12: 40 101.12 - 134.83: 3 134.83 - 168.54: 6 Dihedral angle restraints: 7497 sinusoidal: 4269 harmonic: 3228 Sorted by residual: dihedral pdb=" O4' U R 248 " pdb=" C1' U R 248 " pdb=" N1 U R 248 " pdb=" C2 U R 248 " ideal model delta sinusoidal sigma weight residual 200.00 76.20 123.80 1 1.50e+01 4.44e-03 6.64e+01 dihedral pdb=" C2 TTP A1206 " pdb=" C1' TTP A1206 " pdb=" N1 TTP A1206 " pdb=" O4' TTP A1206 " ideal model delta sinusoidal sigma weight residual 301.68 160.15 141.54 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" CA PRO A 477 " pdb=" C PRO A 477 " pdb=" N GLY A 478 " pdb=" CA GLY A 478 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 7494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.400: 2041 0.400 - 0.800: 0 0.800 - 1.199: 0 1.199 - 1.599: 0 1.599 - 1.999: 1 Chirality restraints: 2042 Sorted by residual: chirality pdb=" P DA B 29 " pdb=" OP1 DA B 29 " pdb=" OP2 DA B 29 " pdb=" O5' DA B 29 " both_signs ideal model delta sigma weight residual True 2.35 0.35 2.00 2.00e-01 2.50e+01 9.99e+01 chirality pdb=" CA PRO A 713 " pdb=" N PRO A 713 " pdb=" C PRO A 713 " pdb=" CB PRO A 713 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A 5 " pdb=" N ILE A 5 " pdb=" C ILE A 5 " pdb=" CB ILE A 5 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2039 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" CG ASN A 138 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC B 61 " -0.026 2.00e-02 2.50e+03 1.65e-02 6.15e+00 pdb=" N1 DC B 61 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DC B 61 " 0.029 2.00e-02 2.50e+03 pdb=" O2 DC B 61 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DC B 61 " -0.014 2.00e-02 2.50e+03 pdb=" C4 DC B 61 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC B 61 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC B 61 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC B 61 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 282 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C MET A 282 " -0.042 2.00e-02 2.50e+03 pdb=" O MET A 282 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 283 " 0.014 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 84 2.44 - 3.06: 8236 3.06 - 3.67: 20676 3.67 - 4.29: 30295 4.29 - 4.90: 46744 Nonbonded interactions: 106035 Sorted by model distance: nonbonded pdb="MG MG A1201 " pdb=" O1B TTP A1206 " model vdw 1.829 2.170 nonbonded pdb=" OG1 THR A 740 " pdb=" OP2 DA T 33 " model vdw 1.901 3.040 nonbonded pdb=" OG SER A 593 " pdb=" OD2 ASP A 613 " model vdw 1.907 3.040 nonbonded pdb=" O ILE A 251 " pdb=" OG1 THR A 254 " model vdw 1.934 3.040 nonbonded pdb=" N2 DG B 60 " pdb=" O2 DC T 11 " model vdw 1.984 3.120 ... (remaining 106030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.65 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.580 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 0.046 12726 Z= 0.170 Angle : 0.888 41.522 17897 Z= 0.412 Chirality : 0.060 1.999 2042 Planarity : 0.004 0.044 1718 Dihedral : 23.572 168.536 5397 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.43 % Favored : 92.02 % Rotamer: Outliers : 0.30 % Allowed : 20.41 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.18 (0.26), residues: 1103 helix: 1.52 (0.23), residues: 530 sheet: -0.92 (0.60), residues: 63 loop : -1.28 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 615 HIS 0.005 0.001 HIS A 734 PHE 0.018 0.001 PHE A1059 TYR 0.010 0.001 TYR A 330 ARG 0.005 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.11330 ( 577) hydrogen bonds : angle 6.36050 ( 1533) metal coordination : bond 0.01366 ( 16) metal coordination : angle 4.46498 ( 10) covalent geometry : bond 0.00376 (12710) covalent geometry : angle 0.88212 (17887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8250 (tt0) cc_final: 0.8045 (tt0) outliers start: 3 outliers final: 3 residues processed: 100 average time/residue: 0.2856 time to fit residues: 40.1868 Evaluate side-chains 92 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 944 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 154 HIS A 544 HIS A 589 ASN A 894 ASN A 962 GLN A 969 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111951 restraints weight = 18746.780| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.77 r_work: 0.3199 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 12726 Z= 0.290 Angle : 0.936 40.575 17897 Z= 0.434 Chirality : 0.063 1.997 2042 Planarity : 0.005 0.044 1718 Dihedral : 25.616 179.561 3127 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.80 % Favored : 92.75 % Rotamer: Outliers : 2.84 % Allowed : 20.20 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.24 (0.26), residues: 1103 helix: 1.55 (0.23), residues: 540 sheet: -0.95 (0.58), residues: 63 loop : -1.28 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 985 HIS 0.008 0.001 HIS A 734 PHE 0.017 0.002 PHE A 644 TYR 0.012 0.002 TYR A 924 ARG 0.008 0.001 ARG A1038 Details of bonding type rmsd hydrogen bonds : bond 0.05873 ( 577) hydrogen bonds : angle 5.06312 ( 1533) metal coordination : bond 0.01178 ( 16) metal coordination : angle 2.89234 ( 10) covalent geometry : bond 0.00665 (12710) covalent geometry : angle 0.93426 (17887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.228 Fit side-chains REVERT: A 33 ARG cc_start: 0.7577 (tpp80) cc_final: 0.6688 (mmm-85) REVERT: A 96 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7562 (ttp-170) REVERT: A 382 ASP cc_start: 0.7814 (m-30) cc_final: 0.7608 (m-30) REVERT: A 400 GLU cc_start: 0.8301 (tt0) cc_final: 0.8075 (tt0) outliers start: 28 outliers final: 19 residues processed: 115 average time/residue: 0.2808 time to fit residues: 45.5810 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111670 restraints weight = 19014.786| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.77 r_work: 0.3208 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12726 Z= 0.180 Angle : 0.882 40.128 17897 Z= 0.402 Chirality : 0.060 1.985 2042 Planarity : 0.004 0.037 1718 Dihedral : 25.533 176.707 3124 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.89 % Favored : 93.65 % Rotamer: Outliers : 3.25 % Allowed : 19.09 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.34 (0.26), residues: 1103 helix: 1.64 (0.23), residues: 542 sheet: -0.93 (0.53), residues: 69 loop : -1.26 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 661 HIS 0.007 0.001 HIS A 734 PHE 0.013 0.001 PHE A 908 TYR 0.011 0.002 TYR A 723 ARG 0.003 0.000 ARG A 834 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 577) hydrogen bonds : angle 4.79148 ( 1533) metal coordination : bond 0.00758 ( 16) metal coordination : angle 2.43317 ( 10) covalent geometry : bond 0.00404 (12710) covalent geometry : angle 0.88038 (17887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.155 Fit side-chains REVERT: A 33 ARG cc_start: 0.7470 (tpp80) cc_final: 0.6667 (mmm-85) REVERT: A 281 TRP cc_start: 0.6560 (m100) cc_final: 0.6192 (t-100) REVERT: A 373 MET cc_start: 0.8738 (mtp) cc_final: 0.8405 (mtp) REVERT: A 400 GLU cc_start: 0.8286 (tt0) cc_final: 0.8011 (tt0) REVERT: A 607 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: A 697 GLU cc_start: 0.8570 (mp0) cc_final: 0.8339 (mp0) REVERT: A 834 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7811 (mtm-85) REVERT: A 1038 ARG cc_start: 0.7325 (mtp-110) cc_final: 0.7028 (mtm-85) REVERT: A 1059 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7788 (p90) outliers start: 32 outliers final: 21 residues processed: 122 average time/residue: 0.2676 time to fit residues: 46.4037 Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 ASN A 878 HIS A 903 GLN A 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.151467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111348 restraints weight = 18852.607| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.91 r_work: 0.3208 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12726 Z= 0.195 Angle : 0.884 40.162 17897 Z= 0.401 Chirality : 0.060 1.980 2042 Planarity : 0.004 0.037 1718 Dihedral : 25.509 177.966 3124 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.07 % Favored : 93.47 % Rotamer: Outliers : 3.76 % Allowed : 19.59 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.35 (0.26), residues: 1103 helix: 1.63 (0.23), residues: 541 sheet: -0.89 (0.48), residues: 83 loop : -1.23 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 985 HIS 0.007 0.001 HIS A 734 PHE 0.014 0.001 PHE A 908 TYR 0.012 0.002 TYR A 330 ARG 0.002 0.000 ARG A 450 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 577) hydrogen bonds : angle 4.72142 ( 1533) metal coordination : bond 0.00799 ( 16) metal coordination : angle 2.25939 ( 10) covalent geometry : bond 0.00443 (12710) covalent geometry : angle 0.88242 (17887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.087 Fit side-chains REVERT: A 33 ARG cc_start: 0.7647 (tpp80) cc_final: 0.6895 (mmm-85) REVERT: A 281 TRP cc_start: 0.6575 (m100) cc_final: 0.6116 (t-100) REVERT: A 373 MET cc_start: 0.8797 (mtp) cc_final: 0.8394 (mtp) REVERT: A 400 GLU cc_start: 0.8442 (tt0) cc_final: 0.8140 (tt0) REVERT: A 607 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: A 697 GLU cc_start: 0.8751 (mp0) cc_final: 0.8505 (mp0) REVERT: A 834 ARG cc_start: 0.8603 (mtp85) cc_final: 0.7879 (mtm-85) REVERT: A 1001 ARG cc_start: 0.7006 (mmt180) cc_final: 0.6596 (mmt90) REVERT: A 1049 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6519 (mt-10) REVERT: A 1059 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7862 (p90) outliers start: 37 outliers final: 27 residues processed: 124 average time/residue: 0.2599 time to fit residues: 46.1136 Evaluate side-chains 123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 ASN A 903 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111454 restraints weight = 18912.984| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.99 r_work: 0.3208 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12726 Z= 0.190 Angle : 0.882 40.129 17897 Z= 0.399 Chirality : 0.059 1.979 2042 Planarity : 0.004 0.037 1718 Dihedral : 25.499 178.637 3124 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.89 % Favored : 93.65 % Rotamer: Outliers : 3.96 % Allowed : 19.29 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.39 (0.26), residues: 1103 helix: 1.66 (0.23), residues: 543 sheet: -0.83 (0.48), residues: 84 loop : -1.22 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 985 HIS 0.006 0.001 HIS A 734 PHE 0.013 0.001 PHE A 908 TYR 0.011 0.002 TYR A 723 ARG 0.004 0.000 ARG A1038 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 577) hydrogen bonds : angle 4.63910 ( 1533) metal coordination : bond 0.00793 ( 16) metal coordination : angle 2.21033 ( 10) covalent geometry : bond 0.00432 (12710) covalent geometry : angle 0.88094 (17887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7657 (tpp80) cc_final: 0.6970 (mmm-85) REVERT: A 373 MET cc_start: 0.8800 (mtp) cc_final: 0.8362 (mtp) REVERT: A 400 GLU cc_start: 0.8434 (tt0) cc_final: 0.8127 (tt0) REVERT: A 421 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8664 (m) REVERT: A 618 MET cc_start: 0.8863 (tpp) cc_final: 0.8601 (tpp) REVERT: A 697 GLU cc_start: 0.8770 (mp0) cc_final: 0.8520 (mp0) REVERT: A 834 ARG cc_start: 0.8603 (mtp85) cc_final: 0.7894 (mtm-85) REVERT: A 957 GLN cc_start: 0.8463 (mm110) cc_final: 0.8247 (mm110) REVERT: A 981 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7979 (mmmm) REVERT: A 1001 ARG cc_start: 0.6876 (mmt180) cc_final: 0.6453 (mmt90) REVERT: A 1009 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7808 (ttpp) REVERT: A 1059 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7784 (p90) outliers start: 39 outliers final: 28 residues processed: 130 average time/residue: 0.3135 time to fit residues: 58.1298 Evaluate side-chains 125 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 843 TYR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112256 restraints weight = 19192.575| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.83 r_work: 0.3229 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12726 Z= 0.169 Angle : 0.870 40.125 17897 Z= 0.392 Chirality : 0.059 1.978 2042 Planarity : 0.004 0.039 1718 Dihedral : 25.485 179.296 3124 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.98 % Favored : 93.56 % Rotamer: Outliers : 4.16 % Allowed : 19.80 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.41 (0.26), residues: 1103 helix: 1.66 (0.22), residues: 545 sheet: -0.79 (0.47), residues: 84 loop : -1.20 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.005 0.001 HIS A 734 PHE 0.013 0.001 PHE A 908 TYR 0.011 0.002 TYR A 330 ARG 0.002 0.000 ARG A 450 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 577) hydrogen bonds : angle 4.57776 ( 1533) metal coordination : bond 0.00740 ( 16) metal coordination : angle 2.10919 ( 10) covalent geometry : bond 0.00381 (12710) covalent geometry : angle 0.86870 (17887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 1.161 Fit side-chains REVERT: A 33 ARG cc_start: 0.7608 (tpp80) cc_final: 0.6941 (mmm-85) REVERT: A 112 GLN cc_start: 0.8364 (mt0) cc_final: 0.8074 (mt0) REVERT: A 373 MET cc_start: 0.8796 (mtp) cc_final: 0.8380 (mtp) REVERT: A 400 GLU cc_start: 0.8426 (tt0) cc_final: 0.8111 (tt0) REVERT: A 421 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8852 (m) REVERT: A 589 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8264 (t0) REVERT: A 607 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: A 697 GLU cc_start: 0.8750 (mp0) cc_final: 0.8494 (mp0) REVERT: A 834 ARG cc_start: 0.8556 (mtp85) cc_final: 0.7854 (mtm-85) REVERT: A 957 GLN cc_start: 0.8455 (mm110) cc_final: 0.8206 (mm110) REVERT: A 981 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7929 (mmmm) REVERT: A 1001 ARG cc_start: 0.6827 (mmt180) cc_final: 0.6343 (mmt90) REVERT: A 1009 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7692 (ttpp) REVERT: A 1038 ARG cc_start: 0.7544 (ptt180) cc_final: 0.7210 (mtm110) REVERT: A 1059 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7761 (p90) outliers start: 41 outliers final: 31 residues processed: 135 average time/residue: 0.2857 time to fit residues: 54.9243 Evaluate side-chains 135 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 843 TYR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 113 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 17 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN A 903 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114588 restraints weight = 19065.998| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.88 r_work: 0.3269 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12726 Z= 0.135 Angle : 0.853 40.125 17897 Z= 0.382 Chirality : 0.058 1.979 2042 Planarity : 0.004 0.041 1718 Dihedral : 25.447 179.675 3124 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.71 % Favored : 93.93 % Rotamer: Outliers : 2.84 % Allowed : 21.62 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.55 (0.26), residues: 1103 helix: 1.74 (0.22), residues: 549 sheet: -0.73 (0.54), residues: 69 loop : -1.10 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 661 HIS 0.003 0.000 HIS A 734 PHE 0.012 0.001 PHE A 908 TYR 0.011 0.001 TYR A 330 ARG 0.002 0.000 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 577) hydrogen bonds : angle 4.44698 ( 1533) metal coordination : bond 0.00746 ( 16) metal coordination : angle 1.90407 ( 10) covalent geometry : bond 0.00296 (12710) covalent geometry : angle 0.85247 (17887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.255 Fit side-chains REVERT: A 33 ARG cc_start: 0.7403 (tpp80) cc_final: 0.6875 (mmm-85) REVERT: A 112 GLN cc_start: 0.8297 (mt0) cc_final: 0.7978 (mt0) REVERT: A 239 ASN cc_start: 0.8045 (p0) cc_final: 0.7693 (t0) REVERT: A 373 MET cc_start: 0.8814 (mtp) cc_final: 0.8369 (mtp) REVERT: A 400 GLU cc_start: 0.8464 (tt0) cc_final: 0.8159 (tt0) REVERT: A 421 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8708 (m) REVERT: A 607 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: A 697 GLU cc_start: 0.8673 (mp0) cc_final: 0.8423 (mp0) REVERT: A 834 ARG cc_start: 0.8522 (mtp85) cc_final: 0.7812 (mtm-85) REVERT: A 957 GLN cc_start: 0.8436 (mm110) cc_final: 0.8209 (mm110) REVERT: A 981 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7911 (mmmm) REVERT: A 1001 ARG cc_start: 0.6756 (mmt180) cc_final: 0.6142 (mmt90) REVERT: A 1009 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7703 (ttpp) REVERT: A 1038 ARG cc_start: 0.7549 (ptt180) cc_final: 0.7207 (mtm110) REVERT: A 1059 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7665 (p90) outliers start: 28 outliers final: 15 residues processed: 134 average time/residue: 0.3672 time to fit residues: 70.2344 Evaluate side-chains 119 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 843 TYR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain A residue 1059 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 492 GLN A 878 HIS A 903 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108342 restraints weight = 19052.373| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.96 r_work: 0.3145 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 12726 Z= 0.325 Angle : 0.943 40.344 17897 Z= 0.433 Chirality : 0.063 1.973 2042 Planarity : 0.005 0.041 1718 Dihedral : 25.580 179.520 3123 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.26 % Favored : 93.38 % Rotamer: Outliers : 3.45 % Allowed : 21.32 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.17 (0.25), residues: 1103 helix: 1.41 (0.22), residues: 544 sheet: -0.97 (0.47), residues: 84 loop : -1.23 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 856 HIS 0.009 0.002 HIS A 734 PHE 0.018 0.002 PHE A 644 TYR 0.013 0.003 TYR A 924 ARG 0.005 0.001 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.05471 ( 577) hydrogen bonds : angle 4.75032 ( 1533) metal coordination : bond 0.01234 ( 16) metal coordination : angle 2.69117 ( 10) covalent geometry : bond 0.00748 (12710) covalent geometry : angle 0.94126 (17887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 1.294 Fit side-chains REVERT: A 33 ARG cc_start: 0.7465 (tpp80) cc_final: 0.6926 (mmm-85) REVERT: A 373 MET cc_start: 0.8745 (mtp) cc_final: 0.8304 (mtp) REVERT: A 400 GLU cc_start: 0.8310 (tt0) cc_final: 0.8008 (tt0) REVERT: A 607 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: A 697 GLU cc_start: 0.8615 (mp0) cc_final: 0.8043 (mp0) REVERT: A 834 ARG cc_start: 0.8501 (mtp85) cc_final: 0.7864 (mtm-85) REVERT: A 957 GLN cc_start: 0.8282 (mm110) cc_final: 0.8025 (mm-40) REVERT: A 981 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7829 (mmmm) REVERT: A 1001 ARG cc_start: 0.6874 (mmt180) cc_final: 0.6306 (mmt90) REVERT: A 1046 GLN cc_start: 0.7541 (mp10) cc_final: 0.7191 (mt0) REVERT: A 1059 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7895 (p90) outliers start: 34 outliers final: 24 residues processed: 124 average time/residue: 0.2803 time to fit residues: 49.3745 Evaluate side-chains 120 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 93 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A 903 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113406 restraints weight = 19002.016| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.81 r_work: 0.3228 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12726 Z= 0.148 Angle : 0.869 40.179 17897 Z= 0.391 Chirality : 0.058 1.981 2042 Planarity : 0.004 0.042 1718 Dihedral : 25.487 179.146 3123 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.26 % Favored : 94.38 % Rotamer: Outliers : 2.13 % Allowed : 23.25 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.41 (0.26), residues: 1103 helix: 1.63 (0.22), residues: 549 sheet: -0.82 (0.48), residues: 84 loop : -1.17 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 521 HIS 0.006 0.001 HIS A1039 PHE 0.013 0.001 PHE A 908 TYR 0.010 0.001 TYR A 723 ARG 0.012 0.000 ARG A1038 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 577) hydrogen bonds : angle 4.54783 ( 1533) metal coordination : bond 0.00879 ( 16) metal coordination : angle 2.19953 ( 10) covalent geometry : bond 0.00330 (12710) covalent geometry : angle 0.86774 (17887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.064 Fit side-chains REVERT: A 33 ARG cc_start: 0.7355 (tpp80) cc_final: 0.6821 (mmm-85) REVERT: A 239 ASN cc_start: 0.8005 (p0) cc_final: 0.7681 (t0) REVERT: A 373 MET cc_start: 0.8756 (mtp) cc_final: 0.8332 (mtp) REVERT: A 400 GLU cc_start: 0.8251 (tt0) cc_final: 0.7950 (tt0) REVERT: A 421 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8724 (m) REVERT: A 697 GLU cc_start: 0.8581 (mp0) cc_final: 0.8301 (mp0) REVERT: A 834 ARG cc_start: 0.8427 (mtp85) cc_final: 0.7793 (mtm-85) REVERT: A 981 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7870 (mmmm) REVERT: A 1001 ARG cc_start: 0.6813 (mmt180) cc_final: 0.6269 (mmt90) REVERT: A 1040 TYR cc_start: 0.7796 (m-80) cc_final: 0.7590 (m-80) REVERT: A 1046 GLN cc_start: 0.7428 (mp10) cc_final: 0.7121 (mt0) REVERT: A 1059 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7636 (p90) outliers start: 21 outliers final: 14 residues processed: 112 average time/residue: 0.2891 time to fit residues: 46.0654 Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1059 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN A 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.153079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113326 restraints weight = 18967.109| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.82 r_work: 0.3231 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12726 Z= 0.153 Angle : 0.874 40.202 17897 Z= 0.390 Chirality : 0.058 1.973 2042 Planarity : 0.004 0.041 1718 Dihedral : 25.398 178.018 3123 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.35 % Favored : 94.29 % Rotamer: Outliers : 1.93 % Allowed : 24.06 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1103 helix: 1.70 (0.22), residues: 549 sheet: -0.70 (0.48), residues: 84 loop : -1.09 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 661 HIS 0.003 0.001 HIS A 734 PHE 0.013 0.001 PHE A 908 TYR 0.010 0.001 TYR A 330 ARG 0.004 0.000 ARG A1038 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 577) hydrogen bonds : angle 4.44769 ( 1533) metal coordination : bond 0.00732 ( 16) metal coordination : angle 2.08053 ( 10) covalent geometry : bond 0.00344 (12710) covalent geometry : angle 0.87283 (17887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7349 (tpp80) cc_final: 0.6856 (mmm-85) REVERT: A 373 MET cc_start: 0.8771 (mtp) cc_final: 0.8325 (mtp) REVERT: A 400 GLU cc_start: 0.8268 (tt0) cc_final: 0.7946 (tt0) REVERT: A 421 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8759 (m) REVERT: A 697 GLU cc_start: 0.8530 (mp0) cc_final: 0.8259 (mp0) REVERT: A 834 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7782 (mtm-85) REVERT: A 981 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7885 (mmmm) REVERT: A 1046 GLN cc_start: 0.7457 (mp10) cc_final: 0.7198 (mt0) REVERT: A 1059 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7619 (p90) outliers start: 19 outliers final: 15 residues processed: 112 average time/residue: 0.3035 time to fit residues: 47.8248 Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1059 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 6.9990 chunk 35 optimal weight: 0.0770 chunk 37 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A1039 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115725 restraints weight = 19013.335| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.83 r_work: 0.3262 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12726 Z= 0.138 Angle : 0.873 40.155 17897 Z= 0.387 Chirality : 0.058 1.973 2042 Planarity : 0.004 0.042 1718 Dihedral : 25.324 176.841 3123 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.81 % Favored : 94.83 % Rotamer: Outliers : 1.83 % Allowed : 24.06 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.63 (0.26), residues: 1103 helix: 1.78 (0.22), residues: 550 sheet: -0.44 (0.55), residues: 69 loop : -1.08 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 661 HIS 0.004 0.000 HIS A1039 PHE 0.012 0.001 PHE A 908 TYR 0.010 0.001 TYR A 330 ARG 0.014 0.000 ARG A1038 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 577) hydrogen bonds : angle 4.37407 ( 1533) metal coordination : bond 0.00699 ( 16) metal coordination : angle 2.02870 ( 10) covalent geometry : bond 0.00308 (12710) covalent geometry : angle 0.87161 (17887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7469.63 seconds wall clock time: 133 minutes 25.27 seconds (8005.27 seconds total)