Starting phenix.real_space_refine on Thu Sep 26 21:06:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg1_43197/09_2024/8vg1_43197.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg1_43197/09_2024/8vg1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg1_43197/09_2024/8vg1_43197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg1_43197/09_2024/8vg1_43197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg1_43197/09_2024/8vg1_43197.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg1_43197/09_2024/8vg1_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.50, per 1000 atoms: 0.59 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: 4.24 Conformation dependent library (CDL) restraints added in 1.1 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: 7.26 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: 6.14 Time building geometry restraints manager: 4.32 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: 1.740 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 42.740 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.050 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 1.000 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: 1.9361 time to fit residues: 386.3617 Evaluate side-chains 163 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8718 (mtmt) REVERT: C 99 ARG cc_start: 0.8307 (mmp80) cc_final: 0.7928 (mmm-85) REVERT: D 105 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8385 (mm-30) REVERT: E 90 MET cc_start: 0.8933 (mmm) cc_final: 0.8652 (mmt) REVERT: G 13 LYS cc_start: 0.8503 (tttp) cc_final: 0.8292 (tmtm) REVERT: G 95 LYS cc_start: 0.9267 (tmtm) cc_final: 0.9016 (tmtt) REVERT: H 47 GLN cc_start: 0.8737 (mt0) cc_final: 0.8484 (mt0) REVERT: H 83 TYR cc_start: 0.8908 (m-10) cc_final: 0.8650 (m-10) REVERT: H 86 ARG cc_start: 0.8567 (mmt-90) cc_final: 0.8333 (mmt90) REVERT: H 105 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8544 (mm-30) REVERT: H 108 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8243 (mttp) REVERT: O 190 MET cc_start: 0.5881 (tpt) cc_final: 0.4772 (tpt) outliers start: 11 outliers final: 5 residues processed: 164 average time/residue: 1.9533 time to fit residues: 340.3539 Evaluate side-chains 157 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 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 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1518 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= 0.305 Angle : 0.594 6.606 22261 Z= 0.359 Chirality : 0.037 0.180 2507 Planarity : 0.005 0.070 1633 Dihedral : 30.438 162.989 4861 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 2.17 % Allowed : 11.99 % 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: 2.31 (0.27), residues: 910 helix: 2.34 (0.20), residues: 603 sheet: -1.15 (1.24), residues: 12 loop : -0.01 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.002 PHE O 204 TYR 0.011 0.002 TYR F 51 ARG 0.005 0.001 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 174 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8681 (mtmt) REVERT: C 99 ARG cc_start: 0.8411 (mmp80) cc_final: 0.7916 (mmm-85) REVERT: D 105 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8330 (mm-30) REVERT: E 90 MET cc_start: 0.8932 (mmm) cc_final: 0.8646 (mmt) REVERT: G 13 LYS cc_start: 0.8532 (tttp) cc_final: 0.8288 (tmtm) REVERT: G 95 LYS cc_start: 0.9266 (tmtm) cc_final: 0.9006 (tmtt) REVERT: H 33 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7033 (mtp-110) REVERT: H 47 GLN cc_start: 0.8746 (mt0) cc_final: 0.8517 (mt0) REVERT: H 83 TYR cc_start: 0.8940 (m-10) cc_final: 0.8676 (m-10) REVERT: H 86 ARG cc_start: 0.8589 (mmt-90) cc_final: 0.8246 (mmt90) REVERT: O 190 MET cc_start: 0.5840 (tpt) cc_final: 0.4750 (tpt) REVERT: T 299 MET cc_start: 0.7036 (tpp) cc_final: 0.6764 (tmm) outliers start: 17 outliers final: 8 residues processed: 165 average time/residue: 1.9168 time to fit residues: 336.1361 Evaluate side-chains 161 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 76 THR 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 83 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1575 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= 0.272 Angle : 0.591 9.654 22261 Z= 0.357 Chirality : 0.036 0.148 2507 Planarity : 0.004 0.072 1633 Dihedral : 30.464 161.711 4861 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 1.91 % Allowed : 13.39 % 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 (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: 2.40 (0.27), residues: 910 helix: 2.40 (0.20), residues: 603 sheet: -1.35 (1.30), residues: 12 loop : 0.04 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR B 88 ARG 0.006 0.000 ARG D 86 *********************** 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 167 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8680 (mtmt) REVERT: C 99 ARG cc_start: 0.8411 (mmp80) cc_final: 0.7906 (mmm-85) REVERT: D 105 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8351 (mm-30) REVERT: E 90 MET cc_start: 0.8900 (mmm) cc_final: 0.8658 (mmp) REVERT: F 92 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8329 (ttp80) REVERT: G 13 LYS cc_start: 0.8524 (tttp) cc_final: 0.8282 (tmtm) REVERT: G 95 LYS cc_start: 0.9262 (tmtm) cc_final: 0.8998 (tmtt) REVERT: H 33 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7045 (mtp-110) REVERT: H 47 GLN cc_start: 0.8701 (mt0) cc_final: 0.8454 (mt0) REVERT: H 83 TYR cc_start: 0.8909 (m-10) cc_final: 0.8620 (m-10) REVERT: H 86 ARG cc_start: 0.8576 (mmt-90) cc_final: 0.8247 (mmt90) REVERT: H 108 LYS cc_start: 0.8536 (mtpm) cc_final: 0.8063 (mttp) REVERT: O 190 MET cc_start: 0.5781 (tpt) cc_final: 0.4574 (tpt) outliers start: 15 outliers final: 9 residues processed: 159 average time/residue: 1.9532 time to fit residues: 329.5615 Evaluate side-chains 163 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 overall best weight: 1.2524 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1616 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= 0.266 Angle : 0.590 9.117 22261 Z= 0.355 Chirality : 0.036 0.135 2507 Planarity : 0.004 0.072 1633 Dihedral : 30.460 160.607 4861 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 1.79 % Allowed : 14.03 % Favored : 84.18 % 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: 2.44 (0.20), residues: 602 sheet: -1.37 (1.33), residues: 12 loop : 0.06 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 214 HIS 0.003 0.001 HIS O 220 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR B 88 ARG 0.006 0.000 ARG D 86 *********************** 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 168 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8678 (mtmt) REVERT: C 99 ARG cc_start: 0.8377 (mmp80) cc_final: 0.7837 (mmm-85) REVERT: E 90 MET cc_start: 0.8898 (mmm) cc_final: 0.8652 (mmp) REVERT: F 92 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8287 (ttp80) REVERT: G 95 LYS cc_start: 0.9266 (tmtm) cc_final: 0.9036 (tmtt) REVERT: H 33 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7060 (mtp-110) REVERT: H 47 GLN cc_start: 0.8673 (mt0) cc_final: 0.8419 (mt0) REVERT: H 83 TYR cc_start: 0.8908 (m-10) cc_final: 0.8617 (m-10) REVERT: H 86 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.8270 (mmt90) REVERT: H 108 LYS cc_start: 0.8587 (mtpm) cc_final: 0.8080 (mttp) REVERT: O 190 MET cc_start: 0.5819 (tpt) cc_final: 0.4635 (tpt) REVERT: O 253 MET cc_start: 0.5373 (ttm) cc_final: 0.4904 (tpp) outliers start: 14 outliers final: 10 residues processed: 161 average time/residue: 1.9972 time to fit residues: 341.6213 Evaluate side-chains 163 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 106 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15401 Z= 0.254 Angle : 0.584 9.378 22261 Z= 0.353 Chirality : 0.036 0.135 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.448 159.899 4861 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 2.42 % Allowed : 14.29 % 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: 2.49 (0.27), residues: 910 helix: 2.46 (0.21), residues: 603 sheet: -1.33 (1.36), residues: 12 loop : 0.08 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.001 TYR B 88 ARG 0.008 0.000 ARG D 86 *********************** 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 171 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8670 (mtmt) REVERT: C 99 ARG cc_start: 0.8377 (mmp80) cc_final: 0.7829 (mmm-85) REVERT: D 86 ARG cc_start: 0.8786 (mmt90) cc_final: 0.8465 (mmt-90) REVERT: E 90 MET cc_start: 0.8875 (mmm) cc_final: 0.8643 (mmp) REVERT: F 92 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8283 (ttp80) REVERT: G 95 LYS cc_start: 0.9268 (tmtm) cc_final: 0.9035 (tmtt) REVERT: H 33 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7061 (mtp-110) REVERT: H 47 GLN cc_start: 0.8670 (mt0) cc_final: 0.8432 (mt0) REVERT: H 83 TYR cc_start: 0.8908 (m-10) cc_final: 0.8650 (m-10) REVERT: H 86 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.8277 (mmt90) REVERT: H 108 LYS cc_start: 0.8537 (mtpm) cc_final: 0.8048 (mttp) REVERT: O 190 MET cc_start: 0.5778 (tpt) cc_final: 0.4617 (tpt) REVERT: O 253 MET cc_start: 0.5332 (ttm) cc_final: 0.4882 (tpp) outliers start: 19 outliers final: 10 residues processed: 162 average time/residue: 1.9133 time to fit residues: 329.6830 Evaluate side-chains 163 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15401 Z= 0.218 Angle : 0.582 8.671 22261 Z= 0.351 Chirality : 0.035 0.161 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.446 159.730 4861 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 2.17 % Allowed : 14.54 % 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: 2.54 (0.27), residues: 910 helix: 2.52 (0.21), residues: 602 sheet: -1.32 (1.37), residues: 12 loop : 0.10 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.026 0.002 PHE O 204 TYR 0.012 0.001 TYR B 88 ARG 0.006 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 170 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8669 (mtmt) REVERT: C 99 ARG cc_start: 0.8375 (mmp80) cc_final: 0.7825 (mmm-85) REVERT: D 86 ARG cc_start: 0.8779 (mmt90) cc_final: 0.8460 (mmt-90) REVERT: E 90 MET cc_start: 0.8869 (mmm) cc_final: 0.8646 (mmp) REVERT: F 92 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8259 (ttp80) REVERT: G 95 LYS cc_start: 0.9261 (tmtm) cc_final: 0.9025 (tmtt) REVERT: H 33 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7059 (mtp-110) REVERT: H 47 GLN cc_start: 0.8708 (mt0) cc_final: 0.8470 (mt0) REVERT: H 83 TYR cc_start: 0.8898 (m-10) cc_final: 0.8654 (m-10) REVERT: H 86 ARG cc_start: 0.8579 (mmt-90) cc_final: 0.8271 (mmt90) REVERT: H 95 GLN cc_start: 0.9044 (tt0) cc_final: 0.8837 (tt0) REVERT: H 108 LYS cc_start: 0.8533 (mtpm) cc_final: 0.8041 (mttp) REVERT: O 190 MET cc_start: 0.5770 (tpt) cc_final: 0.4614 (tpt) REVERT: O 253 MET cc_start: 0.5357 (ttm) cc_final: 0.4897 (tpp) outliers start: 17 outliers final: 11 residues processed: 161 average time/residue: 1.9818 time to fit residues: 338.8260 Evaluate side-chains 166 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15401 Z= 0.204 Angle : 0.579 8.212 22261 Z= 0.351 Chirality : 0.034 0.136 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.438 159.650 4861 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 14.67 % 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: 2.57 (0.27), residues: 910 helix: 2.53 (0.21), residues: 602 sheet: -1.32 (1.37), residues: 12 loop : 0.11 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.014 0.001 PHE O 204 TYR 0.012 0.001 TYR B 88 ARG 0.006 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 170 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8668 (mtmt) REVERT: C 99 ARG cc_start: 0.8373 (mmp80) cc_final: 0.7823 (mmm-85) REVERT: D 86 ARG cc_start: 0.8776 (mmt90) cc_final: 0.8462 (mmt-90) REVERT: E 90 MET cc_start: 0.8870 (mmm) cc_final: 0.8650 (mmp) REVERT: F 92 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8257 (ttp80) REVERT: G 36 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8425 (mptm) REVERT: G 95 LYS cc_start: 0.9262 (tmtm) cc_final: 0.9025 (tmtt) REVERT: H 33 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7059 (mtp-110) REVERT: H 47 GLN cc_start: 0.8726 (mt0) cc_final: 0.8480 (mt0) REVERT: H 83 TYR cc_start: 0.8898 (m-10) cc_final: 0.8650 (m-10) REVERT: H 86 ARG cc_start: 0.8571 (mmt-90) cc_final: 0.8268 (mmt90) REVERT: H 95 GLN cc_start: 0.9033 (tt0) cc_final: 0.8824 (tt0) REVERT: H 108 LYS cc_start: 0.8529 (mtpm) cc_final: 0.8037 (mttp) REVERT: O 190 MET cc_start: 0.5766 (tpt) cc_final: 0.4613 (tpt) REVERT: O 253 MET cc_start: 0.5430 (ttm) cc_final: 0.4976 (tpp) outliers start: 16 outliers final: 11 residues processed: 160 average time/residue: 2.0661 time to fit residues: 351.2138 Evaluate side-chains 167 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 36 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.006 0.052 15401 Z= 0.327 Angle : 0.604 8.925 22261 Z= 0.364 Chirality : 0.037 0.139 2507 Planarity : 0.005 0.073 1633 Dihedral : 30.528 156.409 4861 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.87 % Favored : 98.02 % Rotamer: Outliers : 2.17 % Allowed : 14.54 % 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: 2.32 (0.27), residues: 910 helix: 2.33 (0.21), residues: 608 sheet: -1.19 (1.41), residues: 12 loop : -0.02 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 199 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.002 PHE E 67 TYR 0.015 0.002 TYR B 88 ARG 0.005 0.000 ARG D 86 *********************** 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 171 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8704 (mtmt) REVERT: C 99 ARG cc_start: 0.8352 (mmp80) cc_final: 0.7819 (mmm-85) REVERT: D 86 ARG cc_start: 0.8811 (mmt90) cc_final: 0.8411 (mmt180) REVERT: E 90 MET cc_start: 0.8926 (mmm) cc_final: 0.8663 (mmt) REVERT: F 92 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8285 (ttp80) REVERT: G 36 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8494 (mptm) REVERT: G 95 LYS cc_start: 0.9270 (tmtm) cc_final: 0.9035 (tmtt) REVERT: H 33 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7064 (mtp-110) REVERT: H 47 GLN cc_start: 0.8687 (mt0) cc_final: 0.8421 (mt0) REVERT: H 83 TYR cc_start: 0.8935 (m-10) cc_final: 0.8668 (m-10) REVERT: H 86 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.8282 (mmt90) REVERT: H 95 GLN cc_start: 0.9055 (tt0) cc_final: 0.8852 (tt0) REVERT: H 108 LYS cc_start: 0.8575 (mtpm) cc_final: 0.8088 (mttp) REVERT: O 190 MET cc_start: 0.5837 (tpt) cc_final: 0.4678 (tpt) REVERT: O 253 MET cc_start: 0.5613 (ttm) cc_final: 0.5183 (tpp) REVERT: T 299 MET cc_start: 0.7094 (tpp) cc_final: 0.6825 (tmm) outliers start: 17 outliers final: 10 residues processed: 162 average time/residue: 2.0609 time to fit residues: 355.3984 Evaluate side-chains 164 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 36 LYS 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 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1795 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= 0.296 Angle : 0.607 10.627 22261 Z= 0.364 Chirality : 0.037 0.140 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.543 156.128 4861 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.79 % Allowed : 15.43 % 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 (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: 2.32 (0.27), residues: 910 helix: 2.33 (0.21), residues: 608 sheet: -1.19 (1.43), residues: 12 loop : -0.01 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 199 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.016 0.002 TYR B 88 ARG 0.005 0.000 ARG D 86 ********************** 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 164 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8703 (mtmt) REVERT: C 99 ARG cc_start: 0.8351 (mmp80) cc_final: 0.7816 (mmm-85) REVERT: D 86 ARG cc_start: 0.8804 (mmt90) cc_final: 0.8406 (mmt180) REVERT: E 90 MET cc_start: 0.8912 (mmm) cc_final: 0.8670 (mmt) REVERT: F 92 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8257 (ttp80) REVERT: G 36 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8491 (mptm) REVERT: G 95 LYS cc_start: 0.9268 (tmtm) cc_final: 0.9034 (tmtt) REVERT: H 33 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7066 (mtp-110) REVERT: H 47 GLN cc_start: 0.8678 (mt0) cc_final: 0.8413 (mt0) REVERT: H 83 TYR cc_start: 0.8919 (m-10) cc_final: 0.8651 (m-10) REVERT: H 86 ARG cc_start: 0.8582 (mmt-90) cc_final: 0.8273 (mmt90) REVERT: H 95 GLN cc_start: 0.9049 (tt0) cc_final: 0.8844 (tt0) REVERT: H 108 LYS cc_start: 0.8560 (mtpm) cc_final: 0.8070 (mttp) REVERT: O 190 MET cc_start: 0.5839 (tpt) cc_final: 0.4682 (tpt) REVERT: O 253 MET cc_start: 0.5608 (ttm) cc_final: 0.5185 (tpp) REVERT: T 299 MET cc_start: 0.7097 (tpp) cc_final: 0.6815 (tmm) outliers start: 14 outliers final: 10 residues processed: 156 average time/residue: 2.0425 time to fit residues: 337.6588 Evaluate side-chains 163 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 36 LYS 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 29 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.126282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076359 restraints weight = 22422.371| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.53 r_work: 0.2761 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15401 Z= 0.256 Angle : 0.601 10.074 22261 Z= 0.362 Chirality : 0.036 0.144 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.544 156.036 4861 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 15.43 % 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: 2.37 (0.27), residues: 910 helix: 2.37 (0.21), residues: 608 sheet: -1.16 (1.44), residues: 12 loop : 0.00 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.005 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5905.42 seconds wall clock time: 105 minutes 27.40 seconds (6327.40 seconds total)