Starting phenix.real_space_refine on Thu Sep 18 04:43:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg1_43197/09_2025/8vg1_43197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg1_43197/09_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_43197/09_2025/8vg1_43197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg1_43197/09_2025/8vg1_43197.map" model { file = "/net/cci-nas-00/data/ceres_data/8vg1_43197/09_2025/8vg1_43197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg1_43197/09_2025/8vg1_43197.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.18, per 1000 atoms: 0.22 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: 1.12 Conformation dependent library (CDL) restraints added in 396.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.39 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: 2.83 Time building geometry restraints manager: 1.57 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.650 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- 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 15405 Z= 0.209 Angle : 0.679 8.079 22267 Z= 0.422 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG E 49 TYR 0.010 0.001 TYR C 50 PHE 0.007 0.001 PHE F 61 TRP 0.014 0.001 TRP O 214 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00476 (15401) covalent geometry : angle 0.67519 (22261) hydrogen bonds : bond 0.09716 ( 867) hydrogen bonds : angle 3.37012 ( 2148) metal coordination : bond 0.01007 ( 4) metal coordination : angle 4.57506 ( 6) *********************** 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 : 0.374 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: 0.9831 time to fit residues: 195.5265 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 : 0.381 ------------------------------------------------------------------------------- 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 108 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.126798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076543 restraints weight = 22576.508| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.57 r_work: 0.2763 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15405 Z= 0.246 Angle : 0.616 7.246 22267 Z= 0.370 Chirality : 0.038 0.142 2507 Planarity : 0.005 0.068 1633 Dihedral : 30.324 170.946 4863 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.54 % Favored : 98.35 % Rotamer: Outliers : 1.28 % Allowed : 10.46 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.27), residues: 910 helix: 2.34 (0.21), residues: 603 sheet: -1.71 (1.10), residues: 12 loop : -0.05 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.011 0.002 TYR F 51 PHE 0.009 0.002 PHE E 67 TRP 0.017 0.002 TRP O 214 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00560 (15401) covalent geometry : angle 0.61325 (22261) hydrogen bonds : bond 0.04672 ( 867) hydrogen bonds : angle 2.92743 ( 2148) metal coordination : bond 0.00582 ( 4) metal coordination : angle 3.59392 ( 6) *********************** 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 170 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8797 (mtmt) REVERT: C 73 ASN cc_start: 0.8508 (m-40) cc_final: 0.8199 (t160) REVERT: C 99 ARG cc_start: 0.8514 (mmp80) cc_final: 0.8022 (mmm-85) REVERT: D 105 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8504 (mm-30) REVERT: E 90 MET cc_start: 0.8973 (mmm) cc_final: 0.8726 (mmt) REVERT: G 13 LYS cc_start: 0.8514 (tttp) cc_final: 0.8201 (tmtm) REVERT: G 95 LYS cc_start: 0.9290 (tmtm) cc_final: 0.9031 (tmtt) REVERT: H 37 TYR cc_start: 0.9373 (m-80) cc_final: 0.9155 (m-80) REVERT: H 47 GLN cc_start: 0.8677 (mt0) cc_final: 0.8426 (mt0) REVERT: H 83 TYR cc_start: 0.8848 (m-10) cc_final: 0.8611 (m-10) REVERT: H 86 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.8279 (mmt90) REVERT: H 105 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8765 (mm-30) REVERT: H 108 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8299 (mttp) REVERT: O 181 MET cc_start: 0.8630 (tmm) cc_final: 0.8163 (ptt) REVERT: O 190 MET cc_start: 0.6343 (tpt) cc_final: 0.5137 (tpt) outliers start: 10 outliers final: 4 residues processed: 165 average time/residue: 0.9563 time to fit residues: 167.0805 Evaluate side-chains 154 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 0.0370 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075465 restraints weight = 22732.545| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.57 r_work: 0.2742 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15405 Z= 0.263 Angle : 0.612 6.443 22267 Z= 0.368 Chirality : 0.038 0.162 2507 Planarity : 0.005 0.070 1633 Dihedral : 30.598 164.053 4861 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 12.24 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.27), residues: 910 helix: 2.28 (0.20), residues: 603 sheet: -1.13 (1.24), residues: 12 loop : 0.02 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 86 TYR 0.012 0.002 TYR F 51 PHE 0.010 0.002 PHE O 204 TRP 0.013 0.002 TRP O 214 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00601 (15401) covalent geometry : angle 0.60936 (22261) hydrogen bonds : bond 0.04766 ( 867) hydrogen bonds : angle 2.90956 ( 2148) metal coordination : bond 0.00722 ( 4) metal coordination : angle 3.27141 ( 6) *********************** 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 173 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8752 (mtmt) REVERT: C 99 ARG cc_start: 0.8626 (mmp80) cc_final: 0.8012 (mmm-85) REVERT: D 105 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8445 (mm-30) REVERT: E 90 MET cc_start: 0.8980 (mmm) cc_final: 0.8702 (mmt) REVERT: F 92 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8374 (ttp80) REVERT: G 13 LYS cc_start: 0.8550 (tttp) cc_final: 0.8277 (tmtm) REVERT: G 95 LYS cc_start: 0.9307 (tmtm) cc_final: 0.9036 (tmtt) REVERT: H 33 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6951 (mtp-110) REVERT: H 47 GLN cc_start: 0.8609 (mt0) cc_final: 0.8355 (mt0) REVERT: H 83 TYR cc_start: 0.8896 (m-10) cc_final: 0.8653 (m-10) REVERT: H 86 ARG cc_start: 0.8654 (mmt-90) cc_final: 0.8311 (mmt90) REVERT: O 190 MET cc_start: 0.6234 (tpt) cc_final: 0.5087 (tpt) REVERT: T 299 MET cc_start: 0.6827 (tpp) cc_final: 0.6587 (tmm) outliers start: 16 outliers final: 6 residues processed: 165 average time/residue: 0.9723 time to fit residues: 169.9765 Evaluate side-chains 162 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 40 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.127218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076950 restraints weight = 22684.666| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.55 r_work: 0.2776 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15405 Z= 0.159 Angle : 0.594 10.810 22267 Z= 0.357 Chirality : 0.035 0.165 2507 Planarity : 0.004 0.071 1633 Dihedral : 30.604 163.068 4861 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 1.79 % Allowed : 13.52 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.27), residues: 910 helix: 2.45 (0.20), residues: 603 sheet: -1.37 (1.29), residues: 12 loop : 0.11 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 262 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE E 67 TRP 0.013 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00347 (15401) covalent geometry : angle 0.59290 (22261) hydrogen bonds : bond 0.04151 ( 867) hydrogen bonds : angle 2.85375 ( 2148) metal coordination : bond 0.00508 ( 4) metal coordination : angle 2.42683 ( 6) *********************** 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 173 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8742 (mtmt) REVERT: C 99 ARG cc_start: 0.8605 (mmp80) cc_final: 0.7993 (mmm-85) REVERT: E 38 PRO cc_start: 0.8858 (Cg_exo) cc_final: 0.8653 (Cg_endo) REVERT: E 90 MET cc_start: 0.8920 (mmm) cc_final: 0.8704 (mmp) REVERT: G 13 LYS cc_start: 0.8552 (tttp) cc_final: 0.8278 (tmtm) REVERT: G 95 LYS cc_start: 0.9283 (tmtm) cc_final: 0.8995 (tmtt) REVERT: H 33 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6920 (mtp-110) REVERT: H 47 GLN cc_start: 0.8591 (mt0) cc_final: 0.8335 (mt0) REVERT: H 83 TYR cc_start: 0.8825 (m-10) cc_final: 0.8581 (m-10) REVERT: H 86 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.8269 (mmt90) REVERT: H 108 LYS cc_start: 0.8515 (mtpm) cc_final: 0.8081 (mttp) REVERT: O 190 MET cc_start: 0.6132 (tpt) cc_final: 0.4865 (tpt) REVERT: T 299 MET cc_start: 0.6777 (tpp) cc_final: 0.6554 (tmm) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.9573 time to fit residues: 167.1547 Evaluate side-chains 167 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 C residue 95 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN 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 55 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.127288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.077215 restraints weight = 22694.046| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.54 r_work: 0.2780 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15405 Z= 0.186 Angle : 0.581 7.427 22267 Z= 0.352 Chirality : 0.035 0.134 2507 Planarity : 0.004 0.072 1633 Dihedral : 30.479 162.007 4861 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 1.66 % Allowed : 13.65 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.27), residues: 910 helix: 2.52 (0.20), residues: 603 sheet: -1.45 (1.32), residues: 12 loop : 0.17 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 33 TYR 0.014 0.001 TYR B 88 PHE 0.010 0.001 PHE E 67 TRP 0.012 0.002 TRP O 214 HIS 0.004 0.001 HIS O 220 Details of bonding type rmsd covalent geometry : bond 0.00418 (15401) covalent geometry : angle 0.57961 (22261) hydrogen bonds : bond 0.03927 ( 867) hydrogen bonds : angle 2.80250 ( 2148) metal coordination : bond 0.00497 ( 4) metal coordination : angle 2.48171 ( 6) *********************** 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 169 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8719 (mtmt) REVERT: C 99 ARG cc_start: 0.8564 (mmp80) cc_final: 0.7927 (mmm-85) REVERT: E 90 MET cc_start: 0.8904 (mmm) cc_final: 0.8681 (mmp) REVERT: G 95 LYS cc_start: 0.9291 (tmtm) cc_final: 0.9030 (tmtt) REVERT: H 33 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6928 (mtp-110) REVERT: H 47 GLN cc_start: 0.8588 (mt0) cc_final: 0.8333 (mt0) REVERT: H 83 TYR cc_start: 0.8832 (m-10) cc_final: 0.8574 (m-10) REVERT: H 86 ARG cc_start: 0.8647 (mmt-90) cc_final: 0.8314 (mmt90) REVERT: H 108 LYS cc_start: 0.8594 (mtpm) cc_final: 0.8120 (mttp) REVERT: O 190 MET cc_start: 0.6111 (tpt) cc_final: 0.4860 (tpt) REVERT: T 299 MET cc_start: 0.6799 (tpp) cc_final: 0.6574 (tmm) outliers start: 13 outliers final: 9 residues processed: 162 average time/residue: 0.9996 time to fit residues: 171.2135 Evaluate side-chains 165 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 45 optimal weight: 0.0170 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 115 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.127526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.077632 restraints weight = 22648.417| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.54 r_work: 0.2787 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15405 Z= 0.163 Angle : 0.578 8.194 22267 Z= 0.350 Chirality : 0.034 0.165 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.476 161.848 4861 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 1.79 % Allowed : 14.16 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.27), residues: 910 helix: 2.57 (0.21), residues: 603 sheet: -1.48 (1.33), residues: 12 loop : 0.20 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 33 TYR 0.010 0.001 TYR F 51 PHE 0.010 0.001 PHE E 67 TRP 0.012 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00357 (15401) covalent geometry : angle 0.57648 (22261) hydrogen bonds : bond 0.03832 ( 867) hydrogen bonds : angle 2.79154 ( 2148) metal coordination : bond 0.00466 ( 4) metal coordination : angle 2.34388 ( 6) *********************** 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 170 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8717 (mtmt) REVERT: C 99 ARG cc_start: 0.8557 (mmp80) cc_final: 0.7915 (mmm-85) REVERT: E 90 MET cc_start: 0.8895 (mmm) cc_final: 0.8677 (mmp) REVERT: G 95 LYS cc_start: 0.9285 (tmtm) cc_final: 0.9020 (tmtt) REVERT: H 33 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6926 (mtp-110) REVERT: H 47 GLN cc_start: 0.8653 (mt0) cc_final: 0.8396 (mt0) REVERT: H 86 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.8302 (mmt90) REVERT: H 108 LYS cc_start: 0.8555 (mtpm) cc_final: 0.8059 (mttp) REVERT: O 190 MET cc_start: 0.6134 (tpt) cc_final: 0.4889 (tpt) REVERT: T 299 MET cc_start: 0.6758 (tpp) cc_final: 0.6540 (tmm) outliers start: 14 outliers final: 9 residues processed: 162 average time/residue: 0.9786 time to fit residues: 167.5375 Evaluate side-chains 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 E residue 133 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 115 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3859 r_free = 0.3859 target = 0.127861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078123 restraints weight = 22578.347| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.61 r_work: 0.2795 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15405 Z= 0.158 Angle : 0.573 9.165 22267 Z= 0.347 Chirality : 0.034 0.182 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.441 161.644 4861 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 2.42 % Allowed : 13.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.27), residues: 910 helix: 2.58 (0.21), residues: 602 sheet: -1.49 (1.34), residues: 12 loop : 0.21 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 33 TYR 0.011 0.001 TYR B 88 PHE 0.012 0.001 PHE O 204 TRP 0.013 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00346 (15401) covalent geometry : angle 0.57239 (22261) hydrogen bonds : bond 0.03741 ( 867) hydrogen bonds : angle 2.76610 ( 2148) metal coordination : bond 0.00423 ( 4) metal coordination : angle 2.23064 ( 6) *********************** 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 178 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8712 (mtmt) REVERT: C 99 ARG cc_start: 0.8558 (mmp80) cc_final: 0.7918 (mmm-85) REVERT: E 90 MET cc_start: 0.8894 (mmm) cc_final: 0.8679 (mmp) REVERT: F 92 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8270 (ttp80) REVERT: G 95 LYS cc_start: 0.9279 (tmtm) cc_final: 0.9012 (tmtt) REVERT: H 33 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6927 (mtp-110) REVERT: H 47 GLN cc_start: 0.8658 (mt0) cc_final: 0.8413 (mt0) REVERT: H 86 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.8303 (mmt90) REVERT: H 108 LYS cc_start: 0.8543 (mtpm) cc_final: 0.8078 (mttp) REVERT: O 190 MET cc_start: 0.6167 (tpt) cc_final: 0.4892 (tpt) REVERT: T 299 MET cc_start: 0.6764 (tpp) cc_final: 0.6543 (tmm) outliers start: 19 outliers final: 10 residues processed: 167 average time/residue: 0.9232 time to fit residues: 163.2576 Evaluate side-chains 167 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 C residue 95 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 92 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.128174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078323 restraints weight = 22545.648| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.53 r_work: 0.2803 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15405 Z= 0.168 Angle : 0.568 9.241 22267 Z= 0.345 Chirality : 0.034 0.134 2507 Planarity : 0.004 0.074 1633 Dihedral : 30.300 160.799 4861 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 1.53 % Allowed : 15.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.28), residues: 910 helix: 2.62 (0.21), residues: 602 sheet: -1.40 (1.36), residues: 12 loop : 0.25 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 33 TYR 0.016 0.001 TYR B 88 PHE 0.010 0.001 PHE E 67 TRP 0.014 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00373 (15401) covalent geometry : angle 0.56674 (22261) hydrogen bonds : bond 0.03661 ( 867) hydrogen bonds : angle 2.72396 ( 2148) metal coordination : bond 0.00463 ( 4) metal coordination : angle 2.40891 ( 6) *********************** 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 168 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8699 (mtmt) REVERT: C 99 ARG cc_start: 0.8563 (mmp80) cc_final: 0.7922 (mmm-85) REVERT: D 86 ARG cc_start: 0.8767 (mmt-90) cc_final: 0.8550 (mmt90) REVERT: E 90 MET cc_start: 0.8914 (mmm) cc_final: 0.8681 (mmp) REVERT: G 95 LYS cc_start: 0.9286 (tmtm) cc_final: 0.8982 (tmtt) REVERT: H 33 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6933 (mtp-110) REVERT: H 47 GLN cc_start: 0.8655 (mt0) cc_final: 0.8405 (mt0) REVERT: H 83 TYR cc_start: 0.8789 (m-10) cc_final: 0.8469 (m-10) REVERT: H 86 ARG cc_start: 0.8592 (mmt-90) cc_final: 0.8251 (mmt90) REVERT: H 108 LYS cc_start: 0.8540 (mtpm) cc_final: 0.8093 (mttp) REVERT: O 190 MET cc_start: 0.6149 (tpt) cc_final: 0.4894 (tpt) outliers start: 12 outliers final: 9 residues processed: 161 average time/residue: 0.9444 time to fit residues: 161.0516 Evaluate side-chains 163 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 133 GLU 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 35 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.127598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077672 restraints weight = 22668.628| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.53 r_work: 0.2790 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15405 Z= 0.191 Angle : 0.581 12.276 22267 Z= 0.349 Chirality : 0.035 0.143 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.290 158.987 4861 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.66 % Allowed : 15.31 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.27), residues: 910 helix: 2.52 (0.21), residues: 608 sheet: -1.28 (1.44), residues: 12 loop : 0.15 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 33 TYR 0.016 0.001 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.014 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00431 (15401) covalent geometry : angle 0.57951 (22261) hydrogen bonds : bond 0.03846 ( 867) hydrogen bonds : angle 2.76051 ( 2148) metal coordination : bond 0.00512 ( 4) metal coordination : angle 2.29960 ( 6) *********************** 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 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8736 (mtmt) REVERT: C 99 ARG cc_start: 0.8572 (mmp80) cc_final: 0.7957 (mmm-85) REVERT: D 86 ARG cc_start: 0.8776 (mmt-90) cc_final: 0.8561 (mmt90) REVERT: E 90 MET cc_start: 0.8912 (mmm) cc_final: 0.8676 (mmp) REVERT: F 25 ASN cc_start: 0.8766 (m110) cc_final: 0.8520 (m-40) REVERT: G 95 LYS cc_start: 0.9297 (tmtm) cc_final: 0.8996 (tmtt) REVERT: H 33 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6950 (mtp-110) REVERT: H 47 GLN cc_start: 0.8681 (mt0) cc_final: 0.8414 (mt0) REVERT: H 86 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.8233 (mmt90) REVERT: H 108 LYS cc_start: 0.8554 (mtpm) cc_final: 0.8103 (mttp) REVERT: O 190 MET cc_start: 0.6116 (tpt) cc_final: 0.4845 (tpt) outliers start: 13 outliers final: 9 residues processed: 158 average time/residue: 0.9703 time to fit residues: 162.2737 Evaluate side-chains 163 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 0.0020 chunk 104 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.127653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.077900 restraints weight = 22507.857| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.51 r_work: 0.2794 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15405 Z= 0.185 Angle : 0.581 10.176 22267 Z= 0.350 Chirality : 0.035 0.139 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.292 158.848 4861 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.66 % Allowed : 15.56 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.27), residues: 910 helix: 2.52 (0.21), residues: 608 sheet: -1.24 (1.47), residues: 12 loop : 0.15 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.015 0.001 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.013 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (15401) covalent geometry : angle 0.58041 (22261) hydrogen bonds : bond 0.03800 ( 867) hydrogen bonds : angle 2.76386 ( 2148) metal coordination : bond 0.00494 ( 4) metal coordination : angle 2.21529 ( 6) ********************** 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 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8737 (mtmt) REVERT: C 99 ARG cc_start: 0.8566 (mmp80) cc_final: 0.7962 (mmm-85) REVERT: D 86 ARG cc_start: 0.8777 (mmt-90) cc_final: 0.8563 (mmt90) REVERT: E 90 MET cc_start: 0.8892 (mmm) cc_final: 0.8673 (mmp) REVERT: G 95 LYS cc_start: 0.9294 (tmtm) cc_final: 0.8992 (tmtt) REVERT: H 33 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6953 (mtp-110) REVERT: H 47 GLN cc_start: 0.8678 (mt0) cc_final: 0.8409 (mt0) REVERT: H 86 ARG cc_start: 0.8560 (mmt-90) cc_final: 0.8233 (mmt90) REVERT: H 108 LYS cc_start: 0.8560 (mtpm) cc_final: 0.8110 (mttp) REVERT: O 190 MET cc_start: 0.6089 (tpt) cc_final: 0.4820 (tpt) outliers start: 13 outliers final: 11 residues processed: 158 average time/residue: 0.9943 time to fit residues: 166.2644 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 : 0.377 ------------------------------------------------------------------------------- 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 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 112 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 C 104 GLN D 63 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.076919 restraints weight = 22623.538| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.54 r_work: 0.2776 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15405 Z= 0.207 Angle : 0.588 9.648 22267 Z= 0.354 Chirality : 0.035 0.134 2507 Planarity : 0.004 0.074 1633 Dihedral : 30.385 154.905 4861 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.40 % Allowed : 15.82 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.27), residues: 910 helix: 2.45 (0.21), residues: 608 sheet: -1.14 (1.51), residues: 12 loop : 0.13 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 33 TYR 0.019 0.002 TYR H 83 PHE 0.009 0.001 PHE E 67 TRP 0.015 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00469 (15401) covalent geometry : angle 0.58644 (22261) hydrogen bonds : bond 0.04022 ( 867) hydrogen bonds : angle 2.78621 ( 2148) metal coordination : bond 0.00619 ( 4) metal coordination : angle 2.23007 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7515.47 seconds wall clock time: 127 minutes 50.71 seconds (7670.71 seconds total)