Starting phenix.real_space_refine on Wed Jan 17 22:38:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/01_2024/8u4v_41899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/01_2024/8u4v_41899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/01_2024/8u4v_41899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/01_2024/8u4v_41899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/01_2024/8u4v_41899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/01_2024/8u4v_41899_updated.pdb" } resolution = 2.99 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= 0.018 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4212 2.51 5 N 1102 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H GLU 252": "OE1" <-> "OE2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6637 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1324 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1735 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Conformer: "B" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} bond proxies already assigned to first conformer: 1761 Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.76 Number of scatterers: 6637 At special positions: 0 Unit cell: (77.964, 96.12, 129.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1292 8.00 N 1102 7.00 C 4212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 113 " distance=2.03 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 219 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 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: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 15 sheets defined 17.4% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 26 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 75 through 100 removed outlier: 3.602A pdb=" N ALA A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 148 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 162 through 182 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 208 through 212 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 114 through 116 No H-bonds generated for 'chain 'H' and resid 114 through 116' Processing helix chain 'H' and resid 131 through 136 removed outlier: 3.588A pdb=" N LEU H 135 " --> pdb=" O TRP H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 228 No H-bonds generated for 'chain 'H' and resid 226 through 228' Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing sheet with id= A, first strand: chain 'A' and resid 31 through 35 Processing sheet with id= B, first strand: chain 'B' and resid 205 through 210 removed outlier: 3.570A pdb=" N GLU B 207 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER B 265 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS B 273 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.912A pdb=" N GLN B 249 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 285 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 29 through 32 Processing sheet with id= E, first strand: chain 'L' and resid 35 through 38 removed outlier: 6.109A pdb=" N LYS L 128 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA L 38 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU L 130 " --> pdb=" O ALA L 38 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.113A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 139 through 143 Processing sheet with id= H, first strand: chain 'L' and resid 169 through 174 Processing sheet with id= I, first strand: chain 'H' and resid 29 through 33 Processing sheet with id= J, first strand: chain 'H' and resid 147 through 149 removed outlier: 6.026A pdb=" N ARG H 64 " --> pdb=" O TRP H 73 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP H 73 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ALA H 66 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU H 71 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 123 through 126 Processing sheet with id= L, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.584A pdb=" N SER H 220 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 191 through 194 removed outlier: 4.792A pdb=" N TYR H 234 " --> pdb=" O VAL H 251 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.523A pdb=" N GLY K 16 " --> pdb=" O LEU K 86 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU K 86 " --> pdb=" O GLY K 16 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU K 18 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASN K 84 " --> pdb=" O LEU K 18 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU K 20 " --> pdb=" O GLN K 82 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLN K 82 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N CYS K 22 " --> pdb=" O TYR K 80 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR K 80 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA K 24 " --> pdb=" O THR K 78 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR K 78 " --> pdb=" O ALA K 24 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 95 through 99 removed outlier: 3.955A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1464 1.33 - 1.45: 1560 1.45 - 1.57: 3717 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 6785 Sorted by residual: bond pdb=" N GLY K 10 " pdb=" CA GLY K 10 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.20e-03 1.18e+04 9.94e+00 bond pdb=" N VAL K 50 " pdb=" CA VAL K 50 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.27e+00 bond pdb=" CCJ AV0 H 301 " pdb=" OBV AV0 H 301 " ideal model delta sigma weight residual 1.374 1.431 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" CA SER L 35 " pdb=" CB SER L 35 " ideal model delta sigma weight residual 1.533 1.489 0.044 1.66e-02 3.63e+03 7.10e+00 bond pdb=" N ILE K 29 " pdb=" CA ILE K 29 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.35e-02 5.49e+03 7.09e+00 ... (remaining 6780 not shown) Histogram of bond angle deviations from ideal: 77.15 - 88.55: 4 88.55 - 99.95: 3 99.95 - 111.36: 3147 111.36 - 122.76: 5147 122.76 - 134.16: 930 Bond angle restraints: 9231 Sorted by residual: angle pdb=" CBR AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 110.70 77.15 33.55 3.00e+00 1.11e-01 1.25e+02 angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBS AV0 H 301 " ideal model delta sigma weight residual 110.52 81.56 28.96 3.00e+00 1.11e-01 9.32e+01 angle pdb=" C ARG K 38 " pdb=" CA ARG K 38 " pdb=" CB ARG K 38 " ideal model delta sigma weight residual 109.38 92.93 16.45 1.80e+00 3.09e-01 8.35e+01 angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBR AV0 H 301 " ideal model delta sigma weight residual 107.79 81.90 25.89 3.00e+00 1.11e-01 7.45e+01 angle pdb=" CBS AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 105.72 80.28 25.44 3.00e+00 1.11e-01 7.19e+01 ... (remaining 9226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 3780 23.10 - 46.19: 246 46.19 - 69.29: 48 69.29 - 92.38: 7 92.38 - 115.48: 8 Dihedral angle restraints: 4089 sinusoidal: 1603 harmonic: 2486 Sorted by residual: dihedral pdb=" C ARG K 38 " pdb=" N ARG K 38 " pdb=" CA ARG K 38 " pdb=" CB ARG K 38 " ideal model delta harmonic sigma weight residual -122.60 -101.94 -20.66 0 2.50e+00 1.60e-01 6.83e+01 dihedral pdb=" CB CYS H 180 " pdb=" SG CYS H 180 " pdb=" SG CYS H 236 " pdb=" CB CYS H 236 " ideal model delta sinusoidal sigma weight residual -86.00 -132.12 46.12 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" C ASN L 163 " pdb=" N ASN L 163 " pdb=" CA ASN L 163 " pdb=" CB ASN L 163 " ideal model delta harmonic sigma weight residual -122.60 -134.49 11.89 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 4086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 985 0.111 - 0.222: 65 0.222 - 0.332: 4 0.332 - 0.443: 1 0.443 - 0.554: 1 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA ASN L 163 " pdb=" N ASN L 163 " pdb=" C ASN L 163 " pdb=" CB ASN L 163 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CA ARG K 38 " pdb=" N ARG K 38 " pdb=" C ARG K 38 " pdb=" CB ARG K 38 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA LYS A 157 " pdb=" N LYS A 157 " pdb=" C LYS A 157 " pdb=" CB LYS A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1053 not shown) Planarity restraints: 1153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 73 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO A 74 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 111 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" CD GLU A 111 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU A 111 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 111 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 184 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C SER L 184 " 0.027 2.00e-02 2.50e+03 pdb=" O SER L 184 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN L 185 " -0.009 2.00e-02 2.50e+03 ... (remaining 1150 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 109 2.63 - 3.20: 5789 3.20 - 3.77: 10316 3.77 - 4.33: 14711 4.33 - 4.90: 24704 Nonbonded interactions: 55629 Sorted by model distance: nonbonded pdb=" O THR H 171 " pdb=" OG1 THR H 175 " model vdw 2.063 2.440 nonbonded pdb=" OG SER L 51 " pdb=" OE1 GLN L 52 " model vdw 2.199 2.440 nonbonded pdb=" O ALA L 178 " pdb=" NE2 GLN L 180 " model vdw 2.287 2.520 nonbonded pdb=" CBS AV0 H 301 " pdb=" OBV AV0 H 301 " model vdw 2.334 2.752 nonbonded pdb=" O SER L 119 " pdb=" OG SER H 85 " model vdw 2.354 2.440 ... (remaining 55624 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=0.47 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: 1.490 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: 0.000 Extract box with map and model: 5.830 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.310 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.006 0.057 6785 Z= 0.385 Angle : 1.121 33.548 9231 Z= 0.618 Chirality : 0.060 0.554 1056 Planarity : 0.004 0.060 1153 Dihedral : 16.562 115.481 2483 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.83 % Allowed : 21.47 % Favored : 77.70 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.30), residues: 853 helix: 2.16 (0.43), residues: 139 sheet: 0.22 (0.29), residues: 344 loop : 0.13 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.013 0.001 PHE K 37 TYR 0.007 0.001 TYR H 121 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.784 Fit side-chains REVERT: A 52 MET cc_start: 0.8997 (ptp) cc_final: 0.8581 (ptt) REVERT: A 78 GLN cc_start: 0.7249 (tt0) cc_final: 0.6797 (mt0) REVERT: B 250 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7697 (tttp) REVERT: L 49 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7058 (ttp-110) REVERT: L 130 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7976 (mt-10) REVERT: L 147 ASP cc_start: 0.8481 (p0) cc_final: 0.8261 (m-30) REVERT: L 210 ASP cc_start: 0.8229 (t0) cc_final: 0.7545 (t0) REVERT: H 250 LYS cc_start: 0.8816 (tttm) cc_final: 0.8561 (tptt) REVERT: H 252 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8906 (mt-10) REVERT: K 89 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: K 101 ASP cc_start: 0.8254 (t0) cc_final: 0.7948 (t0) outliers start: 6 outliers final: 1 residues processed: 149 average time/residue: 1.1876 time to fit residues: 185.9570 Evaluate side-chains 114 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain K residue 89 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 GLN K 3 GLN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6785 Z= 0.330 Angle : 0.907 31.901 9231 Z= 0.380 Chirality : 0.044 0.172 1056 Planarity : 0.004 0.050 1153 Dihedral : 8.872 90.882 1056 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.29 % Allowed : 20.22 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.00 (0.30), residues: 853 helix: 2.26 (0.42), residues: 139 sheet: 0.47 (0.29), residues: 351 loop : 0.38 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 125 HIS 0.002 0.001 HIS H 127 PHE 0.015 0.002 PHE B 261 TYR 0.015 0.001 TYR K 104 ARG 0.004 0.001 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.722 Fit side-chains REVERT: A 29 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: A 52 MET cc_start: 0.8993 (ptp) cc_final: 0.8601 (ptt) REVERT: A 78 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: A 130 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7856 (mm) REVERT: B 250 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7890 (tttp) REVERT: B 295 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7320 (mm-40) REVERT: L 49 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7311 (ttp-110) REVERT: L 106 GLU cc_start: 0.8855 (pm20) cc_final: 0.8607 (pm20) REVERT: L 130 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: L 147 ASP cc_start: 0.8335 (p0) cc_final: 0.8091 (m-30) REVERT: L 175 VAL cc_start: 0.9019 (m) cc_final: 0.8617 (t) REVERT: L 210 ASP cc_start: 0.8241 (t0) cc_final: 0.7535 (t0) REVERT: H 178 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8228 (mp) REVERT: H 239 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8087 (t0) REVERT: H 246 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8499 (mmmt) REVERT: H 252 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8792 (mt-10) REVERT: K 44 GLU cc_start: 0.8726 (pm20) cc_final: 0.8248 (pm20) REVERT: K 89 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: K 101 ASP cc_start: 0.8396 (t0) cc_final: 0.7959 (t0) outliers start: 31 outliers final: 8 residues processed: 127 average time/residue: 1.1883 time to fit residues: 158.5686 Evaluate side-chains 119 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain H residue 246 LYS Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 21 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 115 GLN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 GLN H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6785 Z= 0.238 Angle : 0.865 32.346 9231 Z= 0.354 Chirality : 0.042 0.143 1056 Planarity : 0.004 0.055 1153 Dihedral : 7.341 91.351 1055 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.16 % Allowed : 22.16 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.21 (0.31), residues: 853 helix: 2.46 (0.43), residues: 139 sheet: 0.60 (0.29), residues: 349 loop : 0.52 (0.36), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.002 0.000 HIS H 127 PHE 0.011 0.001 PHE B 261 TYR 0.009 0.001 TYR B 264 ARG 0.004 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 0.746 Fit side-chains REVERT: A 29 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: A 52 MET cc_start: 0.9011 (ptp) cc_final: 0.8620 (ptt) REVERT: A 130 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7964 (mm) REVERT: A 159 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 250 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7861 (tttp) REVERT: L 49 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7288 (ttp-110) REVERT: L 106 GLU cc_start: 0.8906 (pm20) cc_final: 0.8655 (pm20) REVERT: L 120 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7211 (mp) REVERT: L 210 ASP cc_start: 0.8242 (t0) cc_final: 0.8027 (t0) REVERT: L 238 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: H 239 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8047 (t0) REVERT: H 246 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8543 (mmmt) REVERT: H 252 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8702 (mt-10) REVERT: K 4 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6152 (pp) REVERT: K 44 GLU cc_start: 0.8793 (pm20) cc_final: 0.8223 (pm20) REVERT: K 89 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: K 101 ASP cc_start: 0.8371 (t0) cc_final: 0.8081 (t0) outliers start: 30 outliers final: 11 residues processed: 121 average time/residue: 1.1681 time to fit residues: 148.7418 Evaluate side-chains 121 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain H residue 246 LYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6785 Z= 0.269 Angle : 0.861 32.082 9231 Z= 0.353 Chirality : 0.041 0.151 1056 Planarity : 0.004 0.042 1153 Dihedral : 7.323 92.701 1055 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.57 % Allowed : 22.44 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.30), residues: 853 helix: 2.40 (0.43), residues: 139 sheet: 0.60 (0.28), residues: 350 loop : 0.58 (0.37), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 PHE 0.012 0.001 PHE B 261 TYR 0.011 0.001 TYR B 264 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 0.698 Fit side-chains REVERT: A 29 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8726 (mtt) REVERT: A 52 MET cc_start: 0.9063 (ptp) cc_final: 0.8647 (ptt) REVERT: A 73 LEU cc_start: 0.7658 (tp) cc_final: 0.7361 (tt) REVERT: A 130 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7872 (mm) REVERT: A 159 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 250 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7865 (tttp) REVERT: L 49 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7340 (ttp-110) REVERT: L 106 GLU cc_start: 0.8906 (pm20) cc_final: 0.8639 (pm20) REVERT: L 120 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7191 (mp) REVERT: H 252 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8679 (mt-10) REVERT: K 4 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6067 (pp) REVERT: K 44 GLU cc_start: 0.8805 (pm20) cc_final: 0.8278 (pm20) REVERT: K 88 PRO cc_start: 0.9031 (Cg_exo) cc_final: 0.8732 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: K 101 ASP cc_start: 0.8397 (t0) cc_final: 0.7856 (t0) outliers start: 33 outliers final: 14 residues processed: 121 average time/residue: 1.0739 time to fit residues: 136.6347 Evaluate side-chains 121 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 195 ASP Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6785 Z= 0.215 Angle : 0.848 31.915 9231 Z= 0.345 Chirality : 0.041 0.145 1056 Planarity : 0.003 0.040 1153 Dihedral : 7.281 92.903 1055 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.74 % Allowed : 22.99 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.29 (0.31), residues: 853 helix: 2.47 (0.44), residues: 139 sheet: 0.64 (0.28), residues: 349 loop : 0.60 (0.37), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 PHE 0.011 0.001 PHE B 261 TYR 0.009 0.001 TYR B 264 ARG 0.002 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.859 Fit side-chains REVERT: A 29 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8722 (mtt) REVERT: A 52 MET cc_start: 0.9061 (ptp) cc_final: 0.8671 (ptt) REVERT: A 130 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 159 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 250 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7861 (tttp) REVERT: L 49 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7347 (ttp-110) REVERT: L 120 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7233 (mp) REVERT: H 239 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.7993 (t0) REVERT: H 252 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8632 (mt-10) REVERT: K 4 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6029 (pp) REVERT: K 12 VAL cc_start: 0.7754 (t) cc_final: 0.7529 (m) REVERT: K 44 GLU cc_start: 0.8773 (pm20) cc_final: 0.8252 (pm20) REVERT: K 88 PRO cc_start: 0.9007 (Cg_exo) cc_final: 0.8712 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: K 101 ASP cc_start: 0.8431 (t0) cc_final: 0.7976 (t0) outliers start: 27 outliers final: 14 residues processed: 119 average time/residue: 1.2679 time to fit residues: 158.6172 Evaluate side-chains 122 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6785 Z= 0.225 Angle : 0.849 31.807 9231 Z= 0.345 Chirality : 0.041 0.145 1056 Planarity : 0.003 0.039 1153 Dihedral : 7.270 92.870 1055 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.02 % Allowed : 22.99 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.21 (0.30), residues: 853 helix: 2.22 (0.44), residues: 142 sheet: 0.68 (0.28), residues: 349 loop : 0.51 (0.36), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS H 61 PHE 0.012 0.001 PHE B 316 TYR 0.009 0.001 TYR A 67 ARG 0.002 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.845 Fit side-chains REVERT: A 29 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: A 52 MET cc_start: 0.9061 (ptp) cc_final: 0.8668 (ptt) REVERT: A 73 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6987 (tt) REVERT: A 78 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: A 130 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7968 (mm) REVERT: A 159 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 250 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7842 (tttp) REVERT: L 49 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7364 (ttp-110) REVERT: L 95 ASP cc_start: 0.7986 (m-30) cc_final: 0.7262 (m-30) REVERT: L 125 GLN cc_start: 0.8767 (mp10) cc_final: 0.8517 (mp10) REVERT: H 252 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8676 (mt-10) REVERT: K 4 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6111 (pp) REVERT: K 12 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7520 (m) REVERT: K 44 GLU cc_start: 0.8783 (pm20) cc_final: 0.8285 (pm20) REVERT: K 88 PRO cc_start: 0.9006 (Cg_exo) cc_final: 0.8703 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8243 (pm20) cc_final: 0.7877 (pm20) REVERT: K 101 ASP cc_start: 0.8420 (t0) cc_final: 0.7930 (t0) outliers start: 29 outliers final: 14 residues processed: 122 average time/residue: 1.1798 time to fit residues: 151.6219 Evaluate side-chains 125 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 68 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6785 Z= 0.185 Angle : 0.841 31.690 9231 Z= 0.340 Chirality : 0.040 0.144 1056 Planarity : 0.004 0.039 1153 Dihedral : 7.102 92.705 1052 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.43 % Allowed : 22.99 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.28 (0.31), residues: 853 helix: 2.30 (0.44), residues: 142 sheet: 0.70 (0.28), residues: 351 loop : 0.56 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.010 0.001 PHE B 316 TYR 0.007 0.001 TYR L 61 ARG 0.010 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 0.780 Fit side-chains REVERT: A 29 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8808 (mtt) REVERT: A 52 MET cc_start: 0.9040 (ptp) cc_final: 0.8694 (ptt) REVERT: A 73 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7136 (tt) REVERT: A 78 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7245 (mt0) REVERT: A 130 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7868 (mm) REVERT: A 159 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 182 CYS cc_start: 0.7604 (m) cc_final: 0.7257 (m) REVERT: B 250 LYS cc_start: 0.8375 (ttpt) cc_final: 0.7844 (tttp) REVERT: B 295 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7340 (tp40) REVERT: L 49 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7390 (ttp-110) REVERT: L 95 ASP cc_start: 0.7968 (m-30) cc_final: 0.7267 (m-30) REVERT: L 125 GLN cc_start: 0.8721 (mp10) cc_final: 0.8423 (mp10) REVERT: H 252 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8634 (mt-10) REVERT: K 4 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6036 (pp) REVERT: K 12 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7574 (m) REVERT: K 44 GLU cc_start: 0.8805 (pm20) cc_final: 0.8299 (pm20) REVERT: K 62 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: K 88 PRO cc_start: 0.8993 (Cg_exo) cc_final: 0.8677 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: K 101 ASP cc_start: 0.8486 (t0) cc_final: 0.8022 (t0) outliers start: 32 outliers final: 13 residues processed: 127 average time/residue: 1.1596 time to fit residues: 155.0852 Evaluate side-chains 126 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.0060 chunk 15 optimal weight: 0.0000 chunk 51 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN K 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6785 Z= 0.298 Angle : 0.865 31.765 9231 Z= 0.356 Chirality : 0.042 0.144 1056 Planarity : 0.004 0.040 1153 Dihedral : 7.202 92.564 1052 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.74 % Allowed : 23.41 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.24 (0.30), residues: 853 helix: 2.18 (0.44), residues: 142 sheet: 0.71 (0.28), residues: 346 loop : 0.54 (0.36), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.002 0.001 HIS H 127 PHE 0.014 0.001 PHE B 261 TYR 0.009 0.001 TYR K 104 ARG 0.010 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.768 Fit side-chains REVERT: A 29 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8664 (mtt) REVERT: A 52 MET cc_start: 0.9067 (ptp) cc_final: 0.8683 (ptt) REVERT: A 73 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7091 (tt) REVERT: A 78 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7257 (mt0) REVERT: A 130 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 159 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 182 CYS cc_start: 0.7588 (m) cc_final: 0.7260 (m) REVERT: B 250 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7656 (tttp) REVERT: L 49 ARG cc_start: 0.8033 (ttp-170) cc_final: 0.7340 (ttp-110) REVERT: L 95 ASP cc_start: 0.7967 (m-30) cc_final: 0.7255 (m-30) REVERT: H 239 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8046 (t0) REVERT: H 252 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8674 (mt-10) REVERT: K 4 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6263 (pp) REVERT: K 12 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7459 (m) REVERT: K 44 GLU cc_start: 0.8787 (pm20) cc_final: 0.8280 (pm20) REVERT: K 88 PRO cc_start: 0.9012 (Cg_exo) cc_final: 0.8715 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: K 101 ASP cc_start: 0.8434 (t0) cc_final: 0.7931 (t0) outliers start: 27 outliers final: 14 residues processed: 116 average time/residue: 1.1456 time to fit residues: 140.0475 Evaluate side-chains 120 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN H 39 GLN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6785 Z= 0.281 Angle : 0.867 31.777 9231 Z= 0.356 Chirality : 0.042 0.145 1056 Planarity : 0.004 0.040 1153 Dihedral : 7.213 92.498 1052 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.60 % Allowed : 23.55 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.22 (0.30), residues: 853 helix: 2.16 (0.44), residues: 142 sheet: 0.70 (0.28), residues: 345 loop : 0.53 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 PHE 0.013 0.001 PHE B 261 TYR 0.010 0.001 TYR B 264 ARG 0.010 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.808 Fit side-chains REVERT: A 29 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8715 (mtt) REVERT: A 52 MET cc_start: 0.9067 (ptp) cc_final: 0.8676 (ptt) REVERT: A 73 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7147 (tt) REVERT: A 78 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: A 130 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7958 (mm) REVERT: A 159 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 182 CYS cc_start: 0.7586 (m) cc_final: 0.7259 (m) REVERT: B 250 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7696 (tttp) REVERT: L 49 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7345 (ttp-110) REVERT: L 95 ASP cc_start: 0.7956 (m-30) cc_final: 0.7247 (m-30) REVERT: H 239 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8030 (t0) REVERT: H 252 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8674 (mt-10) REVERT: K 4 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6300 (pp) REVERT: K 12 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7478 (m) REVERT: K 44 GLU cc_start: 0.8795 (pm20) cc_final: 0.8289 (pm20) REVERT: K 87 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7935 (mtpm) REVERT: K 101 ASP cc_start: 0.8480 (t0) cc_final: 0.8030 (t0) outliers start: 26 outliers final: 14 residues processed: 116 average time/residue: 1.2059 time to fit residues: 147.2508 Evaluate side-chains 121 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN K 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6785 Z= 0.256 Angle : 0.864 31.728 9231 Z= 0.355 Chirality : 0.041 0.146 1056 Planarity : 0.004 0.041 1153 Dihedral : 7.207 92.314 1052 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.05 % Allowed : 23.68 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.24 (0.30), residues: 853 helix: 2.18 (0.44), residues: 142 sheet: 0.74 (0.28), residues: 344 loop : 0.52 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 PHE 0.012 0.001 PHE B 261 TYR 0.010 0.001 TYR B 264 ARG 0.010 0.000 ARG B 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.711 Fit side-chains REVERT: A 29 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8718 (mtt) REVERT: A 52 MET cc_start: 0.9070 (ptp) cc_final: 0.8676 (ptt) REVERT: A 73 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7168 (tt) REVERT: A 78 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7296 (mt0) REVERT: A 130 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 159 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 182 CYS cc_start: 0.7590 (m) cc_final: 0.7262 (m) REVERT: B 250 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7681 (tttp) REVERT: L 49 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7350 (ttp-110) REVERT: L 95 ASP cc_start: 0.7950 (m-30) cc_final: 0.7245 (m-30) REVERT: H 239 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8008 (t0) REVERT: H 252 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8673 (mt-10) REVERT: K 4 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6321 (pp) REVERT: K 12 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7454 (m) REVERT: K 44 GLU cc_start: 0.8801 (pm20) cc_final: 0.8299 (pm20) REVERT: K 87 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7600 (mtpm) REVERT: K 89 GLU cc_start: 0.8839 (pm20) cc_final: 0.8564 (pp20) REVERT: K 101 ASP cc_start: 0.8512 (t0) cc_final: 0.8077 (t0) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 1.2123 time to fit residues: 146.4407 Evaluate side-chains 121 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN K 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.089408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.067194 restraints weight = 14426.647| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.40 r_work: 0.2596 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6785 Z= 0.205 Angle : 0.850 31.589 9231 Z= 0.346 Chirality : 0.041 0.146 1056 Planarity : 0.004 0.042 1153 Dihedral : 7.128 91.961 1052 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.19 % Allowed : 23.68 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.27 (0.31), residues: 853 helix: 2.25 (0.45), residues: 142 sheet: 0.74 (0.28), residues: 350 loop : 0.52 (0.37), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 18 HIS 0.001 0.000 HIS H 61 PHE 0.011 0.001 PHE B 261 TYR 0.010 0.001 TYR B 286 ARG 0.010 0.000 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.44 seconds wall clock time: 57 minutes 28.23 seconds (3448.23 seconds total)