Starting phenix.real_space_refine on Sun Jan 19 18:25:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg1_43197/01_2025/8vg1_43197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg1_43197/01_2025/8vg1_43197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vg1_43197/01_2025/8vg1_43197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg1_43197/01_2025/8vg1_43197.map" model { file = "/net/cci-nas-00/data/ceres_data/8vg1_43197/01_2025/8vg1_43197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg1_43197/01_2025/8vg1_43197.cif" } resolution = 2.48 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 342 5.49 5 S 27 5.16 5 C 8022 2.51 5 N 2688 2.21 5 O 3354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14434 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "T" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14039 SG CYS T 271 25.471 18.700 101.461 1.00183.13 S ATOM 14058 SG CYS T 274 24.780 19.674 105.145 1.00185.68 S ATOM 14201 SG CYS T 292 28.170 20.609 103.380 1.00170.07 S ATOM 14220 SG CYS T 295 27.451 17.231 104.344 1.00173.94 S Time building chain proxies: 8.04, per 1000 atoms: 0.56 Number of scatterers: 14434 At special positions: 0 Unit cell: (92.928, 122.496, 180.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 342 15.00 O 3354 8.00 N 2688 7.00 C 8022 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: 3.44 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 501 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 295 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 292 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 271 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 274 " Number of angles added : 6 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 66.6% alpha, 3.3% beta 171 base pairs and 317 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.967A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.739A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.657A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.308A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.624A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.955A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.585A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.720A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.527A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.276A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.729A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 186 removed outlier: 3.517A pdb=" N ALA O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.893A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 248 through 251 Processing helix chain 'T' and resid 292 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.916A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.646A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.137A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.729A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.136A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.091A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'O' and resid 191 through 192 removed outlier: 4.585A pdb=" N LEU O 191 " --> pdb=" O TRP O 244 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP O 244 " --> pdb=" O LEU O 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 283 through 284 450 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 317 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3009 1.33 - 1.45: 4676 1.45 - 1.57: 6991 1.57 - 1.69: 682 1.69 - 1.81: 43 Bond restraints: 15401 Sorted by residual: bond pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.67e+00 bond pdb=" N LYS D 30 " pdb=" CA LYS D 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N LYS F 20 " pdb=" CA LYS F 20 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N HIS O 168 " pdb=" CA HIS O 168 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 15396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 20797 1.25 - 2.50: 1232 2.50 - 3.75: 198 3.75 - 5.01: 30 5.01 - 6.26: 4 Bond angle restraints: 22261 Sorted by residual: angle pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sigma weight residual 120.20 124.72 -4.52 1.50e+00 4.44e-01 9.07e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.77 116.12 -5.35 1.93e+00 2.68e-01 7.70e+00 angle pdb=" C2' DT I 161 " pdb=" C1' DT I 161 " pdb=" N1 DT I 161 " ideal model delta sigma weight residual 113.50 117.58 -4.08 1.50e+00 4.44e-01 7.39e+00 angle pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sigma weight residual 120.20 124.18 -3.98 1.50e+00 4.44e-01 7.06e+00 angle pdb=" C2' DC I 110 " pdb=" C1' DC I 110 " pdb=" N1 DC I 110 " ideal model delta sigma weight residual 113.50 117.38 -3.88 1.50e+00 4.44e-01 6.68e+00 ... (remaining 22256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 6834 33.52 - 67.03: 1602 67.03 - 100.55: 31 100.55 - 134.07: 0 134.07 - 167.59: 2 Dihedral angle restraints: 8469 sinusoidal: 5771 harmonic: 2698 Sorted by residual: dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 52.41 167.59 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 63.87 156.13 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1505 0.028 - 0.057: 590 0.057 - 0.085: 304 0.085 - 0.113: 87 0.113 - 0.142: 21 Chirality restraints: 2507 Sorted by residual: chirality pdb=" CA VAL T 304 " pdb=" N VAL T 304 " pdb=" C VAL T 304 " pdb=" CB VAL T 304 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" P DC J 94 " pdb=" OP1 DC J 94 " pdb=" OP2 DC J 94 " pdb=" O5' DC J 94 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2504 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO O 238 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " -0.035 2.00e-02 2.50e+03 1.45e-02 6.34e+00 pdb=" N9 DG I 131 " 0.031 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " 0.009 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 131 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 131 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 131 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 138 " -0.027 2.00e-02 2.50e+03 1.16e-02 4.02e+00 pdb=" N9 DG I 138 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG I 138 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 138 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 138 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 138 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I 138 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 138 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 138 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 138 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 138 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 138 " 0.008 2.00e-02 2.50e+03 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4211 2.86 - 3.37: 12501 3.37 - 3.88: 28858 3.88 - 4.39: 33533 4.39 - 4.90: 45718 Nonbonded interactions: 124821 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.351 3.040 nonbonded pdb=" OE2 GLU H 113 " pdb=" NH1 ARG T 320 " model vdw 2.371 3.120 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.375 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.377 3.040 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.407 3.120 ... (remaining 124816 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 40.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15401 Z= 0.254 Angle : 0.675 6.258 22261 Z= 0.421 Chirality : 0.039 0.142 2507 Planarity : 0.005 0.064 1633 Dihedral : 26.205 167.585 6729 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.32 % Favored : 98.57 % Rotamer: Outliers : 0.51 % Allowed : 2.93 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.27), residues: 910 helix: 2.38 (0.21), residues: 588 sheet: -0.78 (1.29), residues: 12 loop : -0.25 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 214 HIS 0.003 0.001 HIS A 113 PHE 0.007 0.001 PHE F 61 TYR 0.010 0.001 TYR C 50 ARG 0.003 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8408 (ttpt) REVERT: B 79 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8552 (mtmt) REVERT: C 99 ARG cc_start: 0.8284 (mmp80) cc_final: 0.7988 (mmm-85) REVERT: D 59 MET cc_start: 0.9329 (tpp) cc_final: 0.9115 (tpp) REVERT: D 86 ARG cc_start: 0.8662 (mmt90) cc_final: 0.8447 (mmt90) REVERT: D 105 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8321 (mm-30) REVERT: D 113 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8599 (mm-30) REVERT: E 79 LYS cc_start: 0.8704 (tttp) cc_final: 0.8479 (ttpt) REVERT: E 90 MET cc_start: 0.8888 (mmm) cc_final: 0.8667 (mmp) REVERT: G 13 LYS cc_start: 0.8475 (tttp) cc_final: 0.8171 (tmtm) REVERT: G 41 GLU cc_start: 0.8520 (tt0) cc_final: 0.8239 (tt0) REVERT: G 95 LYS cc_start: 0.9240 (tmtm) cc_final: 0.9003 (tmtt) REVERT: H 37 TYR cc_start: 0.9482 (m-80) cc_final: 0.9218 (m-80) REVERT: H 47 GLN cc_start: 0.8712 (mt0) cc_final: 0.8420 (mt0) REVERT: H 59 MET cc_start: 0.9396 (tpp) cc_final: 0.9008 (tpp) REVERT: H 76 GLU cc_start: 0.8865 (tp30) cc_final: 0.8647 (tp30) REVERT: H 86 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.8222 (mmt90) REVERT: H 105 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8515 (mm-30) REVERT: H 108 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8233 (mttp) REVERT: O 181 MET cc_start: 0.8472 (tmm) cc_final: 0.8098 (ptt) REVERT: O 190 MET cc_start: 0.6002 (tpt) cc_final: 0.4846 (tpt) outliers start: 4 outliers final: 2 residues processed: 188 average time/residue: 2.0533 time to fit residues: 409.2508 Evaluate side-chains 163 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 63 ASN G 24 GLN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.126115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075880 restraints weight = 22603.986| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.57 r_work: 0.2748 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15401 Z= 0.353 Angle : 0.628 7.400 22261 Z= 0.378 Chirality : 0.039 0.143 2507 Planarity : 0.005 0.067 1633 Dihedral : 30.590 168.026 4863 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.40 % Allowed : 10.46 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.27), residues: 910 helix: 2.27 (0.21), residues: 603 sheet: -1.61 (1.08), residues: 12 loop : -0.09 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP O 214 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.002 PHE E 67 TYR 0.012 0.002 TYR F 51 ARG 0.006 0.001 ARG O 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8790 (mtmt) REVERT: C 99 ARG cc_start: 0.8531 (mmp80) cc_final: 0.8025 (mmm-85) REVERT: D 105 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8492 (mm-30) REVERT: E 90 MET cc_start: 0.8991 (mmm) cc_final: 0.8723 (mmt) REVERT: G 13 LYS cc_start: 0.8541 (tttp) cc_final: 0.8282 (tmtm) REVERT: G 95 LYS cc_start: 0.9291 (tmtm) cc_final: 0.9025 (tmtt) REVERT: H 47 GLN cc_start: 0.8667 (mt0) cc_final: 0.8416 (mt0) REVERT: H 83 TYR cc_start: 0.8858 (m-10) cc_final: 0.8613 (m-10) REVERT: H 86 ARG cc_start: 0.8641 (mmt-90) cc_final: 0.8394 (mmt90) REVERT: H 105 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8786 (mm-30) REVERT: H 108 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8301 (mttp) REVERT: O 190 MET cc_start: 0.6275 (tpt) cc_final: 0.5103 (tpt) outliers start: 11 outliers final: 5 residues processed: 164 average time/residue: 2.0999 time to fit residues: 365.1689 Evaluate side-chains 157 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.126740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.076558 restraints weight = 22750.621| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.54 r_work: 0.2768 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15401 Z= 0.289 Angle : 0.588 6.405 22261 Z= 0.356 Chirality : 0.037 0.175 2507 Planarity : 0.004 0.070 1633 Dihedral : 30.387 163.914 4861 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 1.79 % Allowed : 12.37 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.27), residues: 910 helix: 2.37 (0.20), residues: 602 sheet: -1.16 (1.22), residues: 12 loop : -0.02 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 214 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.002 PHE E 67 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8733 (mtmt) REVERT: C 99 ARG cc_start: 0.8632 (mmp80) cc_final: 0.8029 (mmm-85) REVERT: E 90 MET cc_start: 0.8944 (mmm) cc_final: 0.8697 (mmp) REVERT: G 13 LYS cc_start: 0.8570 (tttp) cc_final: 0.8285 (tmtm) REVERT: G 95 LYS cc_start: 0.9295 (tmtm) cc_final: 0.9019 (tmtt) REVERT: H 33 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6944 (mtp-110) REVERT: H 47 GLN cc_start: 0.8690 (mt0) cc_final: 0.8456 (mt0) REVERT: H 83 TYR cc_start: 0.8894 (m-10) cc_final: 0.8655 (m-10) REVERT: H 86 ARG cc_start: 0.8666 (mmt-90) cc_final: 0.8309 (mmt90) REVERT: O 190 MET cc_start: 0.6226 (tpt) cc_final: 0.5071 (tpt) REVERT: T 299 MET cc_start: 0.6802 (tpp) cc_final: 0.6569 (tmm) outliers start: 14 outliers final: 5 residues processed: 164 average time/residue: 2.0747 time to fit residues: 361.3833 Evaluate side-chains 160 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 115 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.127554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077437 restraints weight = 22448.972| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.53 r_work: 0.2785 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15401 Z= 0.200 Angle : 0.582 9.966 22261 Z= 0.352 Chirality : 0.035 0.160 2507 Planarity : 0.004 0.072 1633 Dihedral : 30.408 163.217 4861 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 2.17 % Allowed : 12.88 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.27), residues: 910 helix: 2.50 (0.21), residues: 602 sheet: -1.30 (1.28), residues: 12 loop : 0.06 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.010 0.001 TYR F 51 ARG 0.005 0.000 ARG O 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8701 (mtmt) REVERT: C 99 ARG cc_start: 0.8611 (mmp80) cc_final: 0.7995 (mmm-85) REVERT: E 90 MET cc_start: 0.8892 (mmm) cc_final: 0.8675 (mmp) REVERT: F 92 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8343 (ttp80) REVERT: G 13 LYS cc_start: 0.8552 (tttp) cc_final: 0.8266 (tmtm) REVERT: G 95 LYS cc_start: 0.9279 (tmtm) cc_final: 0.8991 (tmtt) REVERT: H 33 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6927 (mtp-110) REVERT: H 47 GLN cc_start: 0.8658 (mt0) cc_final: 0.8426 (mt0) REVERT: H 83 TYR cc_start: 0.8834 (m-10) cc_final: 0.8564 (m-10) REVERT: H 86 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.8280 (mmt90) REVERT: H 108 LYS cc_start: 0.8533 (mtpm) cc_final: 0.8086 (mttp) REVERT: O 190 MET cc_start: 0.6182 (tpt) cc_final: 0.4874 (tpt) outliers start: 17 outliers final: 9 residues processed: 165 average time/residue: 2.0871 time to fit residues: 364.6660 Evaluate side-chains 168 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 15 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075691 restraints weight = 22709.634| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.55 r_work: 0.2751 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15401 Z= 0.320 Angle : 0.604 9.957 22261 Z= 0.363 Chirality : 0.038 0.137 2507 Planarity : 0.005 0.072 1633 Dihedral : 30.566 157.717 4861 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 14.03 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.27), residues: 910 helix: 2.38 (0.21), residues: 603 sheet: -1.30 (1.35), residues: 12 loop : 0.04 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 214 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.002 PHE E 67 TYR 0.011 0.002 TYR B 88 ARG 0.011 0.001 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8756 (mtmt) REVERT: C 99 ARG cc_start: 0.8591 (mmp80) cc_final: 0.7927 (mmm-85) REVERT: D 86 ARG cc_start: 0.8849 (mmt90) cc_final: 0.8494 (mmt180) REVERT: D 105 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8539 (mm-30) REVERT: E 90 MET cc_start: 0.8962 (mmm) cc_final: 0.8689 (mmt) REVERT: F 92 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8324 (ttp80) REVERT: G 13 LYS cc_start: 0.8600 (tttp) cc_final: 0.8223 (tptp) REVERT: G 95 LYS cc_start: 0.9277 (tmtm) cc_final: 0.9012 (tmtt) REVERT: H 33 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6952 (mtp-110) REVERT: H 47 GLN cc_start: 0.8633 (mt0) cc_final: 0.8382 (mt0) REVERT: H 83 TYR cc_start: 0.8868 (m-10) cc_final: 0.8639 (m-10) REVERT: H 86 ARG cc_start: 0.8665 (mmt-90) cc_final: 0.8320 (mmt90) REVERT: H 108 LYS cc_start: 0.8597 (mtpm) cc_final: 0.8124 (mttp) REVERT: O 190 MET cc_start: 0.6209 (tpt) cc_final: 0.5055 (tpt) outliers start: 16 outliers final: 10 residues processed: 164 average time/residue: 2.0908 time to fit residues: 364.1546 Evaluate side-chains 165 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.126675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.076609 restraints weight = 22782.353| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.54 r_work: 0.2768 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15401 Z= 0.224 Angle : 0.594 9.206 22261 Z= 0.358 Chirality : 0.035 0.136 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.577 157.644 4861 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 2.17 % Allowed : 14.41 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.27), residues: 910 helix: 2.48 (0.21), residues: 603 sheet: -1.32 (1.38), residues: 12 loop : 0.07 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.013 0.001 TYR F 88 ARG 0.013 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8755 (mtmt) REVERT: C 99 ARG cc_start: 0.8548 (mmp80) cc_final: 0.7872 (mmm-85) REVERT: D 86 ARG cc_start: 0.8825 (mmt90) cc_final: 0.8469 (mmt180) REVERT: D 105 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8560 (mm-30) REVERT: E 90 MET cc_start: 0.8927 (mmm) cc_final: 0.8703 (mmp) REVERT: F 92 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8282 (ttp80) REVERT: G 13 LYS cc_start: 0.8595 (tttp) cc_final: 0.8220 (tptp) REVERT: G 95 LYS cc_start: 0.9281 (tmtm) cc_final: 0.9014 (tmtt) REVERT: H 33 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6949 (mtp-110) REVERT: H 47 GLN cc_start: 0.8616 (mt0) cc_final: 0.8358 (mt0) REVERT: H 86 ARG cc_start: 0.8644 (mmt-90) cc_final: 0.8306 (mmt90) REVERT: H 108 LYS cc_start: 0.8576 (mtpm) cc_final: 0.8096 (mttp) REVERT: O 190 MET cc_start: 0.6150 (tpt) cc_final: 0.4927 (tpt) outliers start: 17 outliers final: 11 residues processed: 159 average time/residue: 2.1031 time to fit residues: 354.2733 Evaluate side-chains 165 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 chunk 55 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.126714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076722 restraints weight = 22759.589| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.53 r_work: 0.2770 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15401 Z= 0.238 Angle : 0.587 8.141 22261 Z= 0.355 Chirality : 0.035 0.142 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.540 157.424 4861 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.79 % Allowed : 14.67 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.27), residues: 910 helix: 2.48 (0.21), residues: 603 sheet: -1.37 (1.39), residues: 12 loop : 0.09 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 199 HIS 0.003 0.001 HIS O 220 PHE 0.010 0.001 PHE O 204 TYR 0.013 0.001 TYR B 88 ARG 0.012 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8754 (mtmt) REVERT: C 99 ARG cc_start: 0.8548 (mmp80) cc_final: 0.7868 (mmm-85) REVERT: D 86 ARG cc_start: 0.8823 (mmt90) cc_final: 0.8475 (mmt180) REVERT: D 105 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8548 (mm-30) REVERT: E 90 MET cc_start: 0.8903 (mmm) cc_final: 0.8691 (mmp) REVERT: F 92 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8303 (ttp80) REVERT: G 13 LYS cc_start: 0.8595 (tttp) cc_final: 0.8221 (tptp) REVERT: G 95 LYS cc_start: 0.9281 (tmtm) cc_final: 0.9013 (tmtt) REVERT: H 33 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6960 (mtp-110) REVERT: H 47 GLN cc_start: 0.8620 (mt0) cc_final: 0.8361 (mt0) REVERT: H 86 ARG cc_start: 0.8642 (mmt-90) cc_final: 0.8307 (mmt90) REVERT: H 108 LYS cc_start: 0.8576 (mtpm) cc_final: 0.8098 (mttp) REVERT: O 190 MET cc_start: 0.6134 (tpt) cc_final: 0.4918 (tpt) outliers start: 14 outliers final: 9 residues processed: 157 average time/residue: 2.0787 time to fit residues: 345.9775 Evaluate side-chains 163 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.126858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076897 restraints weight = 22611.755| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.53 r_work: 0.2774 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15401 Z= 0.237 Angle : 0.583 9.370 22261 Z= 0.353 Chirality : 0.035 0.135 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.504 157.088 4861 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 2.30 % Allowed : 14.54 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.27), residues: 910 helix: 2.49 (0.21), residues: 603 sheet: -1.32 (1.41), residues: 12 loop : 0.11 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.014 0.001 TYR B 88 ARG 0.007 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8750 (mtmt) REVERT: C 99 ARG cc_start: 0.8551 (mmp80) cc_final: 0.7878 (mmm-85) REVERT: D 86 ARG cc_start: 0.8819 (mmt90) cc_final: 0.8565 (mmt-90) REVERT: D 105 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8571 (mm-30) REVERT: E 90 MET cc_start: 0.8906 (mmm) cc_final: 0.8698 (mmp) REVERT: F 92 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8294 (ttp80) REVERT: G 95 LYS cc_start: 0.9282 (tmtm) cc_final: 0.9015 (tmtt) REVERT: H 33 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.6954 (mtp-110) REVERT: H 47 GLN cc_start: 0.8660 (mt0) cc_final: 0.8421 (mt0) REVERT: H 86 ARG cc_start: 0.8645 (mmt-90) cc_final: 0.8316 (mmt90) REVERT: H 108 LYS cc_start: 0.8566 (mtpm) cc_final: 0.8083 (mttp) REVERT: O 190 MET cc_start: 0.6120 (tpt) cc_final: 0.4907 (tpt) outliers start: 18 outliers final: 9 residues processed: 162 average time/residue: 2.0644 time to fit residues: 354.6415 Evaluate side-chains 162 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.126581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.076692 restraints weight = 22616.118| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.55 r_work: 0.2769 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15401 Z= 0.275 Angle : 0.587 8.789 22261 Z= 0.355 Chirality : 0.036 0.134 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.439 155.455 4861 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 14.80 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.27), residues: 910 helix: 2.41 (0.21), residues: 608 sheet: -1.24 (1.45), residues: 12 loop : 0.04 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.015 0.002 TYR B 88 ARG 0.006 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8769 (mtmt) REVERT: C 99 ARG cc_start: 0.8530 (mmp80) cc_final: 0.7880 (mmm-85) REVERT: D 86 ARG cc_start: 0.8828 (mmt90) cc_final: 0.8484 (mmt180) REVERT: D 105 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8566 (mm-30) REVERT: E 90 MET cc_start: 0.8918 (mmm) cc_final: 0.8676 (mmt) REVERT: F 92 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8291 (ttp80) REVERT: G 95 LYS cc_start: 0.9285 (tmtm) cc_final: 0.9018 (tmtt) REVERT: H 33 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6960 (mtp-110) REVERT: H 47 GLN cc_start: 0.8645 (mt0) cc_final: 0.8405 (mt0) REVERT: H 86 ARG cc_start: 0.8653 (mmt-90) cc_final: 0.8322 (mmt90) REVERT: H 108 LYS cc_start: 0.8566 (mtpm) cc_final: 0.8081 (mttp) REVERT: O 190 MET cc_start: 0.6142 (tpt) cc_final: 0.4928 (tpt) REVERT: O 253 MET cc_start: 0.5967 (ttm) cc_final: 0.5559 (tpp) outliers start: 15 outliers final: 10 residues processed: 158 average time/residue: 2.0797 time to fit residues: 348.5248 Evaluate side-chains 162 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 216 ASN Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.127036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.077179 restraints weight = 22614.033| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.52 r_work: 0.2779 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15401 Z= 0.210 Angle : 0.596 14.426 22261 Z= 0.356 Chirality : 0.034 0.156 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.452 155.405 4861 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.79 % Allowed : 15.56 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.27), residues: 910 helix: 2.48 (0.21), residues: 608 sheet: -1.23 (1.46), residues: 12 loop : 0.07 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 199 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.015 0.001 TYR B 88 ARG 0.007 0.000 ARG D 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8763 (mtmt) REVERT: C 99 ARG cc_start: 0.8526 (mmp80) cc_final: 0.7873 (mmm-85) REVERT: D 86 ARG cc_start: 0.8818 (mmt90) cc_final: 0.8472 (mmt180) REVERT: D 105 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8571 (mm-30) REVERT: E 90 MET cc_start: 0.8905 (mmm) cc_final: 0.8683 (mmp) REVERT: F 92 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8263 (ttp80) REVERT: G 95 LYS cc_start: 0.9275 (tmtm) cc_final: 0.9005 (tmtt) REVERT: H 33 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6958 (mtp-110) REVERT: H 47 GLN cc_start: 0.8662 (mt0) cc_final: 0.8420 (mt0) REVERT: H 86 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.8304 (mmt90) REVERT: H 108 LYS cc_start: 0.8561 (mtpm) cc_final: 0.8077 (mttp) REVERT: O 190 MET cc_start: 0.6128 (tpt) cc_final: 0.4914 (tpt) REVERT: O 253 MET cc_start: 0.5970 (ttm) cc_final: 0.5584 (tpp) outliers start: 14 outliers final: 11 residues processed: 158 average time/residue: 1.9927 time to fit residues: 334.3582 Evaluate side-chains 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 216 ASN Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075867 restraints weight = 22653.328| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.55 r_work: 0.2754 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15401 Z= 0.309 Angle : 0.602 9.885 22261 Z= 0.362 Chirality : 0.037 0.136 2507 Planarity : 0.004 0.074 1633 Dihedral : 30.530 155.605 4861 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.87 % Favored : 98.02 % Rotamer: Outliers : 1.66 % Allowed : 15.69 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.27), residues: 910 helix: 2.34 (0.21), residues: 608 sheet: -1.21 (1.47), residues: 12 loop : 0.01 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.017 0.002 TYR F 88 ARG 0.007 0.000 ARG D 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13877.02 seconds wall clock time: 246 minutes 15.58 seconds (14775.58 seconds total)