Starting phenix.real_space_refine on Thu Feb 15 05:59:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2024/5u4j_8506_neut_updated.pdb" } resolution = 3.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 339 5.49 5 S 15 5.16 5 C 5794 2.51 5 N 2109 2.21 5 O 3103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e GLU 145": "OE1" <-> "OE2" Residue "l GLU 25": "OE1" <-> "OE2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "v ARG 150": "NH1" <-> "NH2" Residue "v TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 154": "NH1" <-> "NH2" Residue "v ARG 213": "NH1" <-> "NH2" Residue "v GLU 299": "OE1" <-> "OE2" Residue "v GLU 306": "OE1" <-> "OE2" Residue "w ARG 26": "NH1" <-> "NH2" Residue "w GLU 30": "OE1" <-> "OE2" Residue "w ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11360 Number of models: 1 Model: "" Number of chains: 10 Chain: "a" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 6591 Classifications: {'RNA': 307} Modifications used: {'rna2p': 1, 'rna2p_pur': 23, 'rna2p_pyr': 19, 'rna3p': 7, 'rna3p_pur': 144, 'rna3p_pyr': 113} Link IDs: {'rna2p': 43, 'rna3p': 263} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 233 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p': 2, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "c" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 169 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "d" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 523 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "e" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1001 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "z" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 315 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna3p': 14} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "v" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1054 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "w" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Time building chain proxies: 6.91, per 1000 atoms: 0.61 Number of scatterers: 11360 At special positions: 0 Unit cell: (102.598, 114.528, 102.598, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 339 15.00 O 3103 8.00 N 2109 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 872.9 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 5 sheets defined 22.9% alpha, 21.8% beta 97 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'd' and resid 8 through 15 removed outlier: 3.743A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 31 No H-bonds generated for 'chain 'd' and resid 28 through 31' Processing helix chain 'd' and resid 50 through 64 removed outlier: 3.722A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL d 61 " --> pdb=" O GLU d 57 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG d 62 " --> pdb=" O LYS d 58 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE d 64 " --> pdb=" O LYS d 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 68 removed outlier: 3.665A pdb=" N GLN e 61 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 118 removed outlier: 4.027A pdb=" N VAL e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL e 117 " --> pdb=" O ALA e 113 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 144 removed outlier: 4.108A pdb=" N ARG e 138 " --> pdb=" O ILE e 134 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 removed outlier: 3.803A pdb=" N ARG l 9 " --> pdb=" O ASN l 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 140 through 159 removed outlier: 3.544A pdb=" N ARG v 159 " --> pdb=" O TRP v 155 " (cutoff:3.500A) Processing helix chain 'v' and resid 188 through 191 No H-bonds generated for 'chain 'v' and resid 188 through 191' Processing helix chain 'v' and resid 297 through 315 Processing helix chain 'w' and resid 15 through 20 Processing helix chain 'w' and resid 23 through 25 No H-bonds generated for 'chain 'w' and resid 23 through 25' Processing sheet with id= A, first strand: chain 'c' and resid 151 through 155 Processing sheet with id= B, first strand: chain 'e' and resid 46 through 50 removed outlier: 3.809A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY e 40 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU e 13 " --> pdb=" O GLY e 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'e' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'l' and resid 79 through 82 removed outlier: 6.665A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'v' and resid 322 through 326 removed outlier: 8.022A pdb=" N VAL v 198 " --> pdb=" O ILE v 323 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER v 325 " --> pdb=" O VAL v 198 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG v 200 " --> pdb=" O SER v 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY v 197 " --> pdb=" O ALA v 220 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE v 217 " --> pdb=" O GLY v 135 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY v 135 " --> pdb=" O PHE v 217 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS v 182 " --> pdb=" O ILE v 165 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE v 165 " --> pdb=" O LYS v 182 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N SER v 184 " --> pdb=" O THR v 163 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR v 163 " --> pdb=" O SER v 184 " (cutoff:3.500A) 121 hydrogen bonds defined for protein. 342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 240 hydrogen bonds 396 hydrogen bond angles 0 basepair planarities 97 basepair parallelities 206 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 6.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2289 1.34 - 1.45: 4498 1.45 - 1.57: 4797 1.57 - 1.69: 670 1.69 - 1.81: 24 Bond restraints: 12278 Sorted by residual: bond pdb=" N3 G7M a 527 " pdb=" C4 G7M a 527 " ideal model delta sigma weight residual 1.492 1.342 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C2 4OC a1402 " pdb=" N3 4OC a1402 " ideal model delta sigma weight residual 1.507 1.359 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C2 5MC a1407 " pdb=" N3 5MC a1407 " ideal model delta sigma weight residual 1.493 1.354 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" P G7M a 527 " pdb=" OP1 G7M a 527 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" N3 2MG a1516 " pdb=" C4 2MG a1516 " ideal model delta sigma weight residual 1.496 1.360 0.136 2.00e-02 2.50e+03 4.62e+01 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.93: 1491 104.93 - 112.77: 6840 112.77 - 120.61: 5574 120.61 - 128.45: 3799 128.45 - 136.30: 503 Bond angle restraints: 18207 Sorted by residual: angle pdb=" O3' G7M a 527 " pdb=" P C a 528 " pdb=" O5' C a 528 " ideal model delta sigma weight residual 104.00 122.87 -18.87 1.50e+00 4.44e-01 1.58e+02 angle pdb=" C1' G7M a 527 " pdb=" N9 G7M a 527 " pdb=" C8 G7M a 527 " ideal model delta sigma weight residual 94.96 129.44 -34.48 3.00e+00 1.11e-01 1.32e+02 angle pdb=" O3' G a1064 " pdb=" C3' G a1064 " pdb=" C2' G a1064 " ideal model delta sigma weight residual 109.50 121.44 -11.94 1.50e+00 4.44e-01 6.34e+01 angle pdb=" N LYS w 8 " pdb=" CA LYS w 8 " pdb=" C LYS w 8 " ideal model delta sigma weight residual 110.97 102.56 8.41 1.09e+00 8.42e-01 5.95e+01 angle pdb=" C4' A a 533 " pdb=" C3' A a 533 " pdb=" O3' A a 533 " ideal model delta sigma weight residual 109.40 120.28 -10.88 1.50e+00 4.44e-01 5.26e+01 ... (remaining 18202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 6865 35.82 - 71.64: 796 71.64 - 107.47: 106 107.47 - 143.29: 4 143.29 - 179.11: 5 Dihedral angle restraints: 7776 sinusoidal: 6306 harmonic: 1470 Sorted by residual: dihedral pdb=" C5' A a 560 " pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" O3' A a 560 " ideal model delta sinusoidal sigma weight residual 147.00 82.18 64.82 1 8.00e+00 1.56e-02 8.62e+01 dihedral pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" C2' A a 560 " pdb=" C1' A a 560 " ideal model delta sinusoidal sigma weight residual -35.00 26.81 -61.81 1 8.00e+00 1.56e-02 7.91e+01 dihedral pdb=" O4' A a 560 " pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" C2' A a 560 " ideal model delta sinusoidal sigma weight residual 24.00 -29.69 53.69 1 8.00e+00 1.56e-02 6.12e+01 ... (remaining 7773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 2160 0.202 - 0.405: 107 0.405 - 0.607: 2 0.607 - 0.809: 3 0.809 - 1.012: 1 Chirality restraints: 2273 Sorted by residual: chirality pdb=" P C a 528 " pdb=" OP1 C a 528 " pdb=" OP2 C a 528 " pdb=" O5' C a 528 " both_signs ideal model delta sigma weight residual True 2.41 -3.42 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C3' G a1064 " pdb=" C4' G a1064 " pdb=" O3' G a1064 " pdb=" C2' G a1064 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C3' A a 913 " pdb=" C4' A a 913 " pdb=" O3' A a 913 " pdb=" C2' A a 913 " both_signs ideal model delta sigma weight residual False -2.74 -2.04 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 2270 not shown) Planarity restraints: 1065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.085 2.00e-02 2.50e+03 5.03e-01 5.70e+03 pdb=" C4' 5MC a1407 " -0.434 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.597 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.529 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.409 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.246 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.745 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.264 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.772 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " 0.023 2.00e-02 2.50e+03 4.80e-01 5.18e+03 pdb=" C4' 2MG a1516 " -0.385 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " -0.473 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " 0.563 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " 0.387 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " 0.233 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " -0.765 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " -0.294 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " 0.711 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 a1519 " 0.123 2.00e-02 2.50e+03 2.01e-01 4.02e+02 pdb=" N6 MA6 a1519 " -0.347 2.00e-02 2.50e+03 pdb=" C10 MA6 a1519 " 0.114 2.00e-02 2.50e+03 pdb=" C9 MA6 a1519 " 0.110 2.00e-02 2.50e+03 ... (remaining 1062 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 3 2.42 - 3.04: 4989 3.04 - 3.66: 20366 3.66 - 4.28: 30802 4.28 - 4.90: 42361 Nonbonded interactions: 98521 Sorted by model distance: nonbonded pdb=" N4 C a 528 " pdb=" OD1 ASN l 46 " model vdw 1.797 2.520 nonbonded pdb=" CB LYS l 44 " pdb=" CD PRO l 45 " model vdw 2.219 3.840 nonbonded pdb=" O GLY e 108 " pdb=" N ARG e 112 " model vdw 2.249 2.520 nonbonded pdb=" CE LYS w 8 " pdb=" O HIS w 21 " model vdw 2.448 3.440 nonbonded pdb=" O2' U a 921 " pdb=" O THR e 24 " model vdw 2.505 2.440 ... (remaining 98516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 12.710 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 41.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.009 0.150 12278 Z= 0.546 Angle : 1.213 34.477 18207 Z= 0.753 Chirality : 0.103 1.012 2273 Planarity : 0.023 0.503 1065 Dihedral : 23.800 179.111 6842 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.69 % Favored : 93.92 % Rotamer: Outliers : 2.82 % Allowed : 9.65 % Favored : 87.53 % Cbeta Deviations : 0.43 % 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: -2.95 (0.28), residues: 510 helix: -2.54 (0.31), residues: 110 sheet: -0.97 (0.40), residues: 133 loop : -2.22 (0.27), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP v 319 HIS 0.002 0.001 HIS w 21 PHE 0.007 0.001 PHE e 48 TYR 0.009 0.001 TYR l 95 ARG 0.002 0.000 ARG v 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 71 MET cc_start: 0.6939 (ttt) cc_final: 0.6588 (ppp) REVERT: e 95 PHE cc_start: 0.9031 (t80) cc_final: 0.8819 (t80) REVERT: e 122 ASN cc_start: 0.8446 (m-40) cc_final: 0.8067 (m110) REVERT: l 9 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7260 (mtt90) REVERT: l 77 HIS cc_start: 0.7370 (m90) cc_final: 0.7092 (m-70) REVERT: l 112 GLN cc_start: 0.8065 (mt0) cc_final: 0.7738 (mt0) REVERT: w 17 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7620 (tm-30) outliers start: 12 outliers final: 3 residues processed: 133 average time/residue: 0.3429 time to fit residues: 58.9036 Evaluate side-chains 113 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain w residue 17 GLU Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 GLN e 122 ASN l 5 ASN v 214 HIS w 5 GLN w 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12278 Z= 0.278 Angle : 0.774 12.933 18207 Z= 0.418 Chirality : 0.041 0.272 2273 Planarity : 0.007 0.123 1065 Dihedral : 23.873 173.911 5837 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.25 % Rotamer: Outliers : 2.59 % Allowed : 17.65 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.32), residues: 510 helix: -0.13 (0.43), residues: 121 sheet: -0.51 (0.42), residues: 137 loop : -2.13 (0.30), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP v 155 HIS 0.007 0.001 HIS e 89 PHE 0.011 0.002 PHE v 221 TYR 0.011 0.002 TYR d 51 ARG 0.005 0.001 ARG l 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 68 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: e 122 ASN cc_start: 0.8296 (m110) cc_final: 0.8052 (m110) REVERT: l 3 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8566 (p) REVERT: l 10 LYS cc_start: 0.8730 (tttt) cc_final: 0.8252 (tmmt) REVERT: l 98 VAL cc_start: 0.9163 (t) cc_final: 0.8600 (p) REVERT: v 147 MET cc_start: 0.8017 (mtm) cc_final: 0.7608 (mtm) REVERT: w 4 TYR cc_start: 0.8151 (t80) cc_final: 0.7796 (t80) REVERT: w 45 HIS cc_start: 0.7554 (m-70) cc_final: 0.7153 (m-70) outliers start: 11 outliers final: 4 residues processed: 130 average time/residue: 0.3148 time to fit residues: 53.4535 Evaluate side-chains 122 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 49 SER Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain v residue 179 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 20 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN l 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12278 Z= 0.164 Angle : 0.657 12.211 18207 Z= 0.370 Chirality : 0.035 0.257 2273 Planarity : 0.007 0.118 1065 Dihedral : 23.596 174.765 5829 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.14 % Favored : 96.67 % Rotamer: Outliers : 3.76 % Allowed : 19.06 % Favored : 77.18 % 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: -1.19 (0.34), residues: 510 helix: 1.01 (0.48), residues: 120 sheet: -0.50 (0.41), residues: 137 loop : -1.89 (0.32), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP v 155 HIS 0.003 0.001 HIS e 89 PHE 0.008 0.001 PHE v 221 TYR 0.009 0.001 TYR d 51 ARG 0.010 0.001 ARG l 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 51 TYR cc_start: 0.8521 (t80) cc_final: 0.8214 (t80) REVERT: e 50 TYR cc_start: 0.8435 (t80) cc_final: 0.8195 (t80) REVERT: e 111 MET cc_start: 0.8701 (mtm) cc_final: 0.7977 (tpp) REVERT: e 122 ASN cc_start: 0.8347 (m110) cc_final: 0.8089 (m110) REVERT: l 10 LYS cc_start: 0.8843 (tttt) cc_final: 0.8533 (tmmt) REVERT: v 147 MET cc_start: 0.7988 (mtm) cc_final: 0.7494 (mtm) REVERT: w 8 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8363 (mmtt) outliers start: 16 outliers final: 9 residues processed: 133 average time/residue: 0.3129 time to fit residues: 54.6449 Evaluate side-chains 132 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain d residue 49 SER Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 327 VAL Chi-restraints excluded: chain w residue 8 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 50 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12278 Z= 0.170 Angle : 0.651 12.221 18207 Z= 0.368 Chirality : 0.034 0.252 2273 Planarity : 0.007 0.119 1065 Dihedral : 23.521 176.814 5829 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.25 % Rotamer: Outliers : 3.76 % Allowed : 22.59 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.34), residues: 510 helix: 0.88 (0.47), residues: 126 sheet: -0.38 (0.42), residues: 137 loop : -1.74 (0.33), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP v 155 HIS 0.003 0.001 HIS e 89 PHE 0.005 0.001 PHE w 25 TYR 0.012 0.001 TYR w 4 ARG 0.007 0.000 ARG l 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 51 TYR cc_start: 0.8470 (t80) cc_final: 0.8147 (t80) REVERT: e 50 TYR cc_start: 0.8421 (t80) cc_final: 0.8127 (t80) REVERT: e 64 MET cc_start: 0.6887 (tmm) cc_final: 0.6682 (tmm) REVERT: e 68 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8355 (mmm-85) REVERT: e 111 MET cc_start: 0.8636 (mtm) cc_final: 0.7988 (tpp) REVERT: e 122 ASN cc_start: 0.8372 (m110) cc_final: 0.8146 (m110) REVERT: l 3 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8483 (p) REVERT: l 43 LYS cc_start: 0.8538 (pttp) cc_final: 0.8255 (pttm) REVERT: v 147 MET cc_start: 0.7926 (mtm) cc_final: 0.7402 (mtm) REVERT: w 8 LYS cc_start: 0.8425 (mptt) cc_final: 0.8113 (mmtt) outliers start: 16 outliers final: 9 residues processed: 130 average time/residue: 0.3459 time to fit residues: 58.3158 Evaluate side-chains 127 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain d residue 49 SER Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain v residue 179 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 6 GLN l 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 12278 Z= 0.462 Angle : 0.889 12.576 18207 Z= 0.463 Chirality : 0.045 0.315 2273 Planarity : 0.008 0.125 1065 Dihedral : 23.712 178.928 5829 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.31 % Favored : 95.49 % Rotamer: Outliers : 5.41 % Allowed : 21.18 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.33), residues: 510 helix: 0.14 (0.44), residues: 127 sheet: -0.84 (0.43), residues: 126 loop : -1.92 (0.32), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP v 155 HIS 0.005 0.002 HIS v 214 PHE 0.015 0.003 PHE e 48 TYR 0.020 0.002 TYR e 128 ARG 0.009 0.001 ARG l 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 50 TYR cc_start: 0.8527 (t80) cc_final: 0.8125 (t80) REVERT: e 52 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7582 (ttpp) REVERT: e 68 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8491 (mmm-85) REVERT: e 111 MET cc_start: 0.8836 (mtm) cc_final: 0.8124 (tpp) REVERT: e 121 HIS cc_start: 0.9016 (m90) cc_final: 0.8726 (m90) REVERT: l 3 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8758 (p) REVERT: l 10 LYS cc_start: 0.9002 (tttt) cc_final: 0.8654 (tmmt) REVERT: l 31 ARG cc_start: 0.7229 (ttp80) cc_final: 0.5744 (ptp90) REVERT: l 34 CYS cc_start: 0.8555 (t) cc_final: 0.7997 (p) REVERT: l 110 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8183 (mmm-85) REVERT: l 119 VAL cc_start: 0.8966 (t) cc_final: 0.8505 (m) REVERT: v 147 MET cc_start: 0.8031 (mtm) cc_final: 0.7474 (mtm) REVERT: w 45 HIS cc_start: 0.7809 (m-70) cc_final: 0.7369 (m-70) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 0.4034 time to fit residues: 72.0710 Evaluate side-chains 141 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 85 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain v residue 176 ILE Chi-restraints excluded: chain v residue 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN l 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12278 Z= 0.313 Angle : 0.761 12.162 18207 Z= 0.412 Chirality : 0.039 0.270 2273 Planarity : 0.008 0.120 1065 Dihedral : 23.619 179.134 5829 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 5.18 % Allowed : 22.12 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.34), residues: 510 helix: 0.28 (0.45), residues: 128 sheet: -0.90 (0.42), residues: 134 loop : -1.91 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP v 155 HIS 0.003 0.001 HIS e 121 PHE 0.011 0.002 PHE w 25 TYR 0.013 0.002 TYR w 4 ARG 0.012 0.001 ARG w 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 50 TYR cc_start: 0.8432 (t80) cc_final: 0.7967 (t80) REVERT: e 64 MET cc_start: 0.7154 (tmm) cc_final: 0.6782 (tmm) REVERT: e 68 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8465 (mmm-85) REVERT: e 111 MET cc_start: 0.8750 (mtm) cc_final: 0.8075 (tpp) REVERT: e 112 ARG cc_start: 0.8680 (ptm160) cc_final: 0.8313 (ptm160) REVERT: l 3 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8670 (p) REVERT: l 31 ARG cc_start: 0.7213 (ttp80) cc_final: 0.5757 (ptp90) REVERT: l 34 CYS cc_start: 0.8523 (t) cc_final: 0.7932 (p) REVERT: l 110 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8098 (mmm-85) REVERT: l 119 VAL cc_start: 0.9009 (t) cc_final: 0.8523 (m) REVERT: v 147 MET cc_start: 0.8034 (mtm) cc_final: 0.7468 (mtm) REVERT: v 306 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7230 (tm-30) REVERT: w 45 HIS cc_start: 0.7840 (m-70) cc_final: 0.7489 (m-70) outliers start: 22 outliers final: 18 residues processed: 133 average time/residue: 0.3662 time to fit residues: 63.3666 Evaluate side-chains 142 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain v residue 176 ILE Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 325 SER Chi-restraints excluded: chain v residue 327 VAL Chi-restraints excluded: chain w residue 21 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 48 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12278 Z= 0.149 Angle : 0.651 12.169 18207 Z= 0.367 Chirality : 0.033 0.247 2273 Planarity : 0.007 0.118 1065 Dihedral : 23.466 179.838 5829 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.25 % Rotamer: Outliers : 3.76 % Allowed : 24.00 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.34), residues: 510 helix: 0.83 (0.45), residues: 128 sheet: -0.51 (0.41), residues: 144 loop : -1.84 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP v 155 HIS 0.004 0.001 HIS d 41 PHE 0.008 0.001 PHE w 25 TYR 0.016 0.001 TYR w 4 ARG 0.007 0.001 ARG w 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 50 TYR cc_start: 0.8334 (t80) cc_final: 0.7983 (t80) REVERT: e 111 MET cc_start: 0.8606 (mtm) cc_final: 0.8042 (tpp) REVERT: e 112 ARG cc_start: 0.8578 (ptm160) cc_final: 0.8354 (ptm160) REVERT: l 3 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8404 (p) REVERT: l 10 LYS cc_start: 0.8877 (tttt) cc_final: 0.8670 (tmmt) REVERT: l 31 ARG cc_start: 0.7103 (ttp80) cc_final: 0.5636 (ptp90) REVERT: v 147 MET cc_start: 0.7963 (mtm) cc_final: 0.7450 (mtm) REVERT: v 306 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7165 (tm-30) REVERT: w 45 HIS cc_start: 0.7577 (m-70) cc_final: 0.7337 (m-70) outliers start: 16 outliers final: 14 residues processed: 131 average time/residue: 0.3441 time to fit residues: 58.2175 Evaluate side-chains 133 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 0.0570 chunk 69 optimal weight: 0.0060 chunk 73 optimal weight: 3.9990 overall best weight: 1.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12278 Z= 0.246 Angle : 0.698 12.087 18207 Z= 0.385 Chirality : 0.035 0.266 2273 Planarity : 0.008 0.120 1065 Dihedral : 23.431 179.320 5829 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.73 % Favored : 96.08 % Rotamer: Outliers : 4.71 % Allowed : 24.71 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.34), residues: 510 helix: 0.74 (0.45), residues: 128 sheet: -0.57 (0.40), residues: 144 loop : -1.91 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP v 155 HIS 0.003 0.001 HIS d 41 PHE 0.008 0.001 PHE w 25 TYR 0.017 0.001 TYR w 4 ARG 0.010 0.001 ARG l 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 50 TYR cc_start: 0.8431 (t80) cc_final: 0.8007 (t80) REVERT: e 64 MET cc_start: 0.7059 (tmm) cc_final: 0.6716 (tmm) REVERT: e 111 MET cc_start: 0.8655 (mtm) cc_final: 0.8054 (tpp) REVERT: e 112 ARG cc_start: 0.8650 (ptm160) cc_final: 0.8353 (ptm160) REVERT: l 3 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8511 (p) REVERT: l 31 ARG cc_start: 0.7148 (ttp80) cc_final: 0.5684 (ptp90) REVERT: l 110 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8074 (mmm-85) REVERT: v 147 MET cc_start: 0.8003 (mtm) cc_final: 0.7465 (mtm) REVERT: v 306 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7163 (tm-30) REVERT: w 45 HIS cc_start: 0.7737 (m-70) cc_final: 0.7463 (m-70) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.3343 time to fit residues: 54.5170 Evaluate side-chains 130 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain v residue 176 ILE Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 319 TRP Chi-restraints excluded: chain v residue 327 VAL Chi-restraints excluded: chain w residue 21 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12278 Z= 0.198 Angle : 0.673 12.105 18207 Z= 0.374 Chirality : 0.034 0.253 2273 Planarity : 0.007 0.119 1065 Dihedral : 23.415 178.896 5829 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.14 % Favored : 96.67 % Rotamer: Outliers : 4.71 % Allowed : 24.71 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.34), residues: 510 helix: 0.88 (0.45), residues: 128 sheet: -0.56 (0.41), residues: 144 loop : -1.85 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP v 155 HIS 0.002 0.001 HIS d 41 PHE 0.008 0.001 PHE w 25 TYR 0.017 0.001 TYR w 4 ARG 0.011 0.001 ARG l 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 50 TYR cc_start: 0.8422 (t80) cc_final: 0.8000 (t80) REVERT: e 64 MET cc_start: 0.7020 (tmm) cc_final: 0.6701 (tmm) REVERT: e 111 MET cc_start: 0.8616 (mtm) cc_final: 0.8043 (tpp) REVERT: e 112 ARG cc_start: 0.8616 (ptm160) cc_final: 0.8311 (ptm160) REVERT: l 3 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8340 (p) REVERT: l 31 ARG cc_start: 0.7196 (ttp80) cc_final: 0.5688 (ptp90) REVERT: l 110 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8111 (mmm-85) REVERT: v 147 MET cc_start: 0.8004 (mtm) cc_final: 0.7475 (mtm) REVERT: v 225 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7268 (mm-30) REVERT: v 306 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7170 (tm-30) REVERT: w 45 HIS cc_start: 0.7732 (m-70) cc_final: 0.7454 (m-70) outliers start: 20 outliers final: 18 residues processed: 129 average time/residue: 0.3459 time to fit residues: 57.6470 Evaluate side-chains 133 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain v residue 149 GLU Chi-restraints excluded: chain v residue 176 ILE Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 319 TRP Chi-restraints excluded: chain v residue 327 VAL Chi-restraints excluded: chain w residue 21 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.0770 chunk 54 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12278 Z= 0.251 Angle : 0.706 12.068 18207 Z= 0.388 Chirality : 0.035 0.266 2273 Planarity : 0.008 0.120 1065 Dihedral : 23.421 178.468 5829 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.92 % Favored : 95.88 % Rotamer: Outliers : 4.94 % Allowed : 24.71 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.34), residues: 510 helix: 0.75 (0.45), residues: 128 sheet: -0.57 (0.41), residues: 144 loop : -1.87 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP v 155 HIS 0.002 0.001 HIS v 214 PHE 0.009 0.002 PHE w 25 TYR 0.015 0.002 TYR w 4 ARG 0.013 0.001 ARG l 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 50 TYR cc_start: 0.8441 (t80) cc_final: 0.7947 (t80) REVERT: e 64 MET cc_start: 0.7070 (tmm) cc_final: 0.6784 (tmm) REVERT: e 111 MET cc_start: 0.8659 (mtm) cc_final: 0.8048 (tpp) REVERT: e 112 ARG cc_start: 0.8649 (ptm160) cc_final: 0.8334 (ptm160) REVERT: l 3 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8386 (p) REVERT: l 31 ARG cc_start: 0.7131 (ttp80) cc_final: 0.5689 (ptp90) REVERT: l 110 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8079 (mmm-85) REVERT: v 147 MET cc_start: 0.8019 (mtm) cc_final: 0.7489 (mtm) REVERT: v 225 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7390 (mm-30) REVERT: v 306 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7144 (tm-30) REVERT: w 45 HIS cc_start: 0.7805 (m-70) cc_final: 0.7485 (m-70) outliers start: 21 outliers final: 18 residues processed: 125 average time/residue: 0.3533 time to fit residues: 56.9116 Evaluate side-chains 134 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain v residue 149 GLU Chi-restraints excluded: chain v residue 176 ILE Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 319 TRP Chi-restraints excluded: chain v residue 327 VAL Chi-restraints excluded: chain w residue 21 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 40 GLN d 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.160390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.137126 restraints weight = 16249.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.140841 restraints weight = 5528.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.143017 restraints weight = 3127.635| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12278 Z= 0.332 Angle : 0.774 12.238 18207 Z= 0.415 Chirality : 0.038 0.280 2273 Planarity : 0.008 0.122 1065 Dihedral : 23.484 178.104 5829 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.90 % Favored : 94.90 % Rotamer: Outliers : 5.88 % Allowed : 24.24 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.34), residues: 510 helix: 0.32 (0.45), residues: 127 sheet: -0.73 (0.42), residues: 139 loop : -2.01 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP v 155 HIS 0.009 0.002 HIS d 41 PHE 0.009 0.002 PHE w 25 TYR 0.014 0.002 TYR v 129 ARG 0.013 0.001 ARG l 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2110.05 seconds wall clock time: 39 minutes 27.41 seconds (2367.41 seconds total)