Starting phenix.real_space_refine on Fri Jul 19 07:53:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/07_2024/8u4v_41899.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/07_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_41899/07_2024/8u4v_41899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/07_2024/8u4v_41899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/07_2024/8u4v_41899.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/07_2024/8u4v_41899.cif" } 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-dev-5388/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: 4.84, per 1000 atoms: 0.73 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: 3.04 Conformation dependent library (CDL) restraints added in 1.3 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... Secondary structure from input PDB file: 16 helices and 17 sheets defined 20.6% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 5 through 27 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.600A pdb=" N LEU A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 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 110 through 149 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.734A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'B' and resid 267 through 270 removed outlier: 3.666A pdb=" N ASN B 270 " --> pdb=" O ASN B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 270' Processing helix chain 'L' and resid 104 through 108 removed outlier: 4.109A pdb=" N PHE L 108 " --> pdb=" O PRO L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 153 Processing helix chain 'L' and resid 208 through 212 Processing helix chain 'H' and resid 54 through 57 removed outlier: 3.636A pdb=" N SER H 57 " --> pdb=" O ASN H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 57' Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'H' and resid 130 through 137 removed outlier: 3.588A pdb=" N LEU H 135 " --> pdb=" O TRP H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 225 through 229 removed outlier: 3.531A pdb=" N LEU H 229 " --> pdb=" O SER H 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 removed outlier: 4.147A pdb=" N GLY K 57 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 205 through 210 removed outlier: 7.133A pdb=" N ALA B 205 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N HIS B 241 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLU B 207 " --> pdb=" O HIS B 241 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N THR B 243 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 209 " --> pdb=" O THR B 243 " (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=AA3, 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=AA4, first strand: chain 'L' and resid 29 through 32 Processing sheet with id=AA5, first strand: chain 'L' and resid 35 through 38 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=AA6, first strand: chain 'L' and resid 35 through 38 Processing sheet with id=AA7, first strand: chain 'L' and resid 139 through 143 removed outlier: 5.495A pdb=" N TYR L 198 " --> pdb=" O ASN L 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 169 through 174 Processing sheet with id=AA9, first strand: chain 'H' and resid 29 through 33 Processing sheet with id=AB1, first strand: chain 'H' and resid 37 through 38 removed outlier: 4.214A pdb=" N TRP H 125 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR H 59 " --> pdb=" O TRP H 125 " (cutoff:3.500A) 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) Processing sheet with id=AB2, first strand: chain 'H' and resid 37 through 38 Processing sheet with id=AB3, 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) removed outlier: 3.913A pdb=" N ASP H 184 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR H 216 " --> pdb=" O ASP H 184 " (cutoff:3.500A) Processing sheet with id=AB4, 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) removed outlier: 3.913A pdb=" N ASP H 184 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR H 216 " --> pdb=" O ASP H 184 " (cutoff:3.500A) Processing sheet with id=AB5, 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=AB6, first strand: chain 'K' and resid 3 through 6 removed outlier: 6.055A pdb=" N GLY K 16 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 59 through 60 removed outlier: 5.532A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 92 through 93 335 hydrogen bonds defined for protein. 891 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: 2.10 Time building geometry restraints manager: 3.05 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: 108 2.63 - 3.20: 5758 3.20 - 3.77: 10273 3.77 - 4.33: 14642 4.33 - 4.90: 24696 Nonbonded interactions: 55477 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 55472 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: 1.620 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.850 Find NCS groups from input model: 0.080 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- 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= 0.369 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 : 0.677 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: 1.1403 time to fit residues: 178.7912 Evaluate side-chains 114 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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: 0.2980 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 65 optimal weight: 6.9990 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: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN L 115 GLN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 GLN H 211 GLN K 3 GLN K 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6785 Z= 0.198 Angle : 0.884 32.308 9231 Z= 0.366 Chirality : 0.042 0.174 1056 Planarity : 0.004 0.054 1153 Dihedral : 9.211 89.533 1056 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 21.33 % Favored : 75.35 % 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: 1.12 (0.30), residues: 853 helix: 2.47 (0.43), residues: 141 sheet: 0.56 (0.29), residues: 352 loop : 0.37 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 18 HIS 0.002 0.001 HIS H 61 PHE 0.011 0.001 PHE K 37 TYR 0.010 0.001 TYR B 264 ARG 0.004 0.000 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 145 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.697 Fit side-chains REVERT: A 52 MET cc_start: 0.9011 (ptp) cc_final: 0.8605 (ptt) REVERT: A 78 GLN cc_start: 0.7270 (tt0) cc_final: 0.6881 (mt0) REVERT: A 130 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7876 (mm) REVERT: B 250 LYS cc_start: 0.8400 (ttpt) cc_final: 0.7899 (tttp) REVERT: L 49 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7660 (ttp-170) REVERT: L 106 GLU cc_start: 0.8757 (pm20) cc_final: 0.8516 (pm20) REVERT: L 130 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7665 (mt-10) REVERT: L 147 ASP cc_start: 0.8266 (p0) cc_final: 0.8002 (m-30) REVERT: L 175 VAL cc_start: 0.8980 (m) cc_final: 0.8574 (t) REVERT: L 210 ASP cc_start: 0.8184 (t0) cc_final: 0.7554 (t0) REVERT: L 238 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: H 178 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8227 (mp) REVERT: H 239 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.7994 (t0) REVERT: H 246 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8552 (mmmt) REVERT: H 252 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8793 (mt-10) REVERT: K 27 ARG cc_start: 0.8280 (ptp-170) cc_final: 0.8062 (ptp-170) REVERT: K 44 GLU cc_start: 0.8594 (pm20) cc_final: 0.8319 (pm20) REVERT: K 89 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: K 101 ASP cc_start: 0.8371 (t0) cc_final: 0.7947 (t0) REVERT: K 110 TYR cc_start: 0.8410 (m-80) cc_final: 0.8069 (m-80) outliers start: 24 outliers final: 6 residues processed: 130 average time/residue: 1.2341 time to fit residues: 168.5499 Evaluate side-chains 123 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 238 GLU 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 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 21 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7704 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6785 Z= 0.217 Angle : 0.863 32.350 9231 Z= 0.354 Chirality : 0.041 0.141 1056 Planarity : 0.004 0.059 1153 Dihedral : 7.279 90.982 1055 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.02 % Allowed : 21.61 % Favored : 74.38 % 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: 1.31 (0.30), residues: 853 helix: 2.58 (0.43), residues: 141 sheet: 0.69 (0.28), residues: 351 loop : 0.49 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS B 241 PHE 0.010 0.001 PHE B 316 TYR 0.009 0.001 TYR B 264 ARG 0.003 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 141 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.802 Fit side-chains REVERT: A 52 MET cc_start: 0.9015 (ptp) cc_final: 0.8583 (ptt) REVERT: A 78 GLN cc_start: 0.7196 (tt0) cc_final: 0.6798 (mt0) REVERT: A 130 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7888 (mm) REVERT: A 159 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 250 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7810 (tttp) REVERT: L 49 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7255 (ttp-110) REVERT: L 130 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7762 (mt-10) REVERT: L 151 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8408 (ptpp) REVERT: L 175 VAL cc_start: 0.9075 (m) cc_final: 0.8776 (t) REVERT: L 180 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7603 (pt0) REVERT: L 210 ASP cc_start: 0.8226 (t0) cc_final: 0.7835 (t0) REVERT: H 239 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.7998 (t0) REVERT: H 246 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8531 (mmmt) REVERT: K 4 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5712 (pp) REVERT: K 27 ARG cc_start: 0.8351 (ptp-170) cc_final: 0.8147 (ptp-170) REVERT: K 44 GLU cc_start: 0.8737 (pm20) cc_final: 0.8196 (pm20) REVERT: K 89 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: K 101 ASP cc_start: 0.8386 (t0) cc_final: 0.8161 (t0) outliers start: 29 outliers final: 10 residues processed: 125 average time/residue: 1.1964 time to fit residues: 157.2560 Evaluate side-chains 122 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 180 GLN Chi-restraints excluded: chain L residue 204 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6785 Z= 0.207 Angle : 0.859 31.968 9231 Z= 0.349 Chirality : 0.041 0.144 1056 Planarity : 0.004 0.052 1153 Dihedral : 7.219 91.642 1055 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.19 % Allowed : 22.99 % Favored : 73.82 % 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: 1.30 (0.31), residues: 853 helix: 2.40 (0.45), residues: 144 sheet: 0.75 (0.28), residues: 352 loop : 0.47 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 18 HIS 0.001 0.000 HIS B 241 PHE 0.010 0.001 PHE B 261 TYR 0.022 0.001 TYR A 67 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 131 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.763 Fit side-chains REVERT: A 52 MET cc_start: 0.8937 (ptp) cc_final: 0.8548 (ptt) REVERT: A 78 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6837 (mt0) REVERT: A 130 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7934 (mm) REVERT: A 131 MET cc_start: 0.8577 (ttp) cc_final: 0.8368 (ttp) REVERT: B 250 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7784 (tttp) REVERT: L 49 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7351 (ttp-110) REVERT: L 130 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: L 151 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8362 (ptpp) REVERT: L 210 ASP cc_start: 0.8265 (t0) cc_final: 0.7639 (t0) REVERT: H 133 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7746 (mt-10) REVERT: H 178 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8173 (mp) REVERT: H 252 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8525 (mt-10) REVERT: K 4 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5828 (pp) REVERT: K 27 ARG cc_start: 0.8428 (ptp-170) cc_final: 0.8200 (ptp-170) REVERT: K 44 GLU cc_start: 0.8830 (pm20) cc_final: 0.8270 (pm20) REVERT: K 88 PRO cc_start: 0.9037 (Cg_exo) cc_final: 0.8750 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: K 101 ASP cc_start: 0.8466 (t0) cc_final: 0.8010 (t0) outliers start: 23 outliers final: 8 residues processed: 120 average time/residue: 1.3328 time to fit residues: 167.5766 Evaluate side-chains 116 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 174 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6785 Z= 0.292 Angle : 0.875 31.882 9231 Z= 0.360 Chirality : 0.042 0.143 1056 Planarity : 0.004 0.047 1153 Dihedral : 7.323 93.053 1055 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.29 % Allowed : 22.85 % 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: 1.26 (0.30), residues: 853 helix: 2.34 (0.44), residues: 144 sheet: 0.67 (0.28), residues: 352 loop : 0.53 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 125 HIS 0.001 0.001 HIS B 241 PHE 0.013 0.001 PHE B 261 TYR 0.012 0.001 TYR B 264 ARG 0.002 0.000 ARG A 158 *********************** 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 136 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 0.730 Fit side-chains REVERT: A 52 MET cc_start: 0.8996 (ptp) cc_final: 0.8622 (ptt) REVERT: A 75 GLN cc_start: 0.7323 (tm-30) cc_final: 0.6864 (tm-30) REVERT: A 78 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6784 (mt0) REVERT: A 130 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7966 (mm) REVERT: B 250 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7824 (tttp) REVERT: B 292 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6935 (p0) REVERT: L 49 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7358 (ttp-110) REVERT: L 120 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7194 (mp) REVERT: L 130 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: H 133 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7762 (mt-10) REVERT: H 239 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.7990 (t0) REVERT: H 252 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8541 (mt-10) REVERT: K 4 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.5935 (pp) REVERT: K 44 GLU cc_start: 0.8838 (pm20) cc_final: 0.8210 (pm20) REVERT: K 88 PRO cc_start: 0.9045 (Cg_exo) cc_final: 0.8750 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: K 101 ASP cc_start: 0.8400 (t0) cc_final: 0.7957 (t0) outliers start: 31 outliers final: 15 residues processed: 122 average time/residue: 1.1357 time to fit residues: 145.9288 Evaluate side-chains 127 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 B residue 292 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 195 ASP Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 239 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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: 0.7716 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6785 Z= 0.222 Angle : 0.858 31.743 9231 Z= 0.349 Chirality : 0.041 0.144 1056 Planarity : 0.004 0.046 1153 Dihedral : 7.257 92.882 1055 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.74 % Allowed : 22.85 % Favored : 73.41 % 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: 1.32 (0.30), residues: 853 helix: 2.42 (0.44), residues: 144 sheet: 0.73 (0.28), residues: 352 loop : 0.53 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.001 0.000 HIS B 285 PHE 0.010 0.001 PHE B 261 TYR 0.009 0.001 TYR B 264 ARG 0.002 0.000 ARG K 31 *********************** 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: 27 poor density : 108 time to evaluate : 0.745 Fit side-chains REVERT: A 52 MET cc_start: 0.8999 (ptp) cc_final: 0.8599 (ptt) REVERT: A 75 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6848 (tm-30) REVERT: A 78 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: A 130 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7853 (mm) REVERT: B 250 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7815 (tttp) REVERT: B 292 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6926 (p0) REVERT: L 49 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7379 (ttp-110) REVERT: L 95 ASP cc_start: 0.7985 (m-30) cc_final: 0.7247 (m-30) REVERT: L 130 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: H 133 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7763 (mt-10) REVERT: H 252 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8544 (mt-10) REVERT: K 4 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6077 (pp) REVERT: K 30 SER cc_start: 0.8373 (t) cc_final: 0.8141 (m) REVERT: K 31 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8280 (mmm160) REVERT: K 44 GLU cc_start: 0.8741 (pm20) cc_final: 0.8240 (pm20) REVERT: K 88 PRO cc_start: 0.9069 (Cg_exo) cc_final: 0.8793 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8271 (pm20) cc_final: 0.7907 (pm20) REVERT: K 101 ASP cc_start: 0.8442 (t0) cc_final: 0.7952 (t0) outliers start: 27 outliers final: 13 residues processed: 123 average time/residue: 1.2743 time to fit residues: 164.7653 Evaluate side-chains 121 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 292 ASP 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 38 VAL Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 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 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7712 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6785 Z= 0.206 Angle : 0.851 31.717 9231 Z= 0.345 Chirality : 0.041 0.145 1056 Planarity : 0.003 0.044 1153 Dihedral : 7.136 92.808 1052 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.74 % Allowed : 22.85 % Favored : 73.41 % 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: 1.37 (0.31), residues: 853 helix: 2.43 (0.44), residues: 144 sheet: 0.77 (0.28), residues: 352 loop : 0.56 (0.37), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 18 HIS 0.001 0.000 HIS B 241 PHE 0.010 0.001 PHE B 261 TYR 0.008 0.001 TYR K 110 ARG 0.002 0.000 ARG K 53 *********************** 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 133 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.667 Fit side-chains REVERT: A 52 MET cc_start: 0.9002 (ptp) cc_final: 0.8608 (ptt) REVERT: A 75 GLN cc_start: 0.7225 (tm-30) cc_final: 0.6803 (tm-30) REVERT: A 78 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.7108 (mt0) REVERT: A 130 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7951 (mm) REVERT: B 250 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7816 (tttp) REVERT: B 292 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6920 (p0) REVERT: L 49 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7384 (ttp-110) REVERT: L 95 ASP cc_start: 0.7926 (m-30) cc_final: 0.7229 (m-30) REVERT: L 120 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7284 (mp) REVERT: L 130 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: H 133 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7748 (mt-10) REVERT: H 252 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8522 (mt-10) REVERT: K 4 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5945 (pp) REVERT: K 30 SER cc_start: 0.8343 (t) cc_final: 0.8105 (m) REVERT: K 34 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8628 (mmm) REVERT: K 44 GLU cc_start: 0.8777 (pm20) cc_final: 0.8259 (pm20) REVERT: K 88 PRO cc_start: 0.9067 (Cg_exo) cc_final: 0.8759 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8273 (pm20) cc_final: 0.7916 (pm20) REVERT: K 101 ASP cc_start: 0.8484 (t0) cc_final: 0.8004 (t0) outliers start: 27 outliers final: 14 residues processed: 123 average time/residue: 1.1748 time to fit residues: 152.0992 Evaluate side-chains 124 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 B residue 292 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 204 LEU 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 4 LEU Chi-restraints excluded: chain K residue 34 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 6785 Z= 0.417 Angle : 0.907 31.969 9231 Z= 0.379 Chirality : 0.044 0.146 1056 Planarity : 0.004 0.043 1153 Dihedral : 7.382 92.586 1052 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.88 % Allowed : 22.30 % Favored : 73.82 % 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 (0.30), residues: 853 helix: 2.50 (0.44), residues: 141 sheet: 0.64 (0.28), residues: 339 loop : 0.54 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 125 HIS 0.003 0.001 HIS H 61 PHE 0.018 0.002 PHE B 261 TYR 0.013 0.002 TYR K 104 ARG 0.004 0.001 ARG L 133 *********************** 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: 28 poor density : 100 time to evaluate : 0.701 Fit side-chains REVERT: A 52 MET cc_start: 0.9014 (ptp) cc_final: 0.8620 (ptt) REVERT: A 75 GLN cc_start: 0.7332 (tm-30) cc_final: 0.6884 (tm-30) REVERT: A 78 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: A 130 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 250 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7825 (tttp) REVERT: B 292 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6816 (p0) REVERT: L 49 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7356 (ttp-110) REVERT: L 95 ASP cc_start: 0.7979 (m-30) cc_final: 0.7274 (m-30) REVERT: H 252 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8572 (mt-10) REVERT: K 4 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6077 (pp) REVERT: K 30 SER cc_start: 0.8475 (t) cc_final: 0.8196 (m) REVERT: K 34 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8684 (mmm) REVERT: K 44 GLU cc_start: 0.8760 (pm20) cc_final: 0.8222 (pm20) REVERT: K 89 GLU cc_start: 0.8317 (pm20) cc_final: 0.8011 (pm20) REVERT: K 101 ASP cc_start: 0.8374 (t0) cc_final: 0.7808 (t0) outliers start: 28 outliers final: 13 residues processed: 117 average time/residue: 1.2433 time to fit residues: 152.7933 Evaluate side-chains 117 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 235 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU 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 34 MET 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 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN K 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2490 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= 0.215 Angle : 0.864 31.723 9231 Z= 0.353 Chirality : 0.041 0.147 1056 Planarity : 0.004 0.046 1153 Dihedral : 7.240 92.767 1052 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.05 % Allowed : 23.41 % Favored : 73.55 % 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: 1.37 (0.30), residues: 853 helix: 2.69 (0.45), residues: 141 sheet: 0.71 (0.28), residues: 348 loop : 0.54 (0.36), residues: 364 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 0.010 0.001 PHE B 261 TYR 0.018 0.001 TYR K 60 ARG 0.002 0.000 ARG K 53 *********************** 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 125 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.8987 (ptp) cc_final: 0.8599 (ptt) REVERT: A 75 GLN cc_start: 0.7263 (tm-30) cc_final: 0.6819 (tm-30) REVERT: A 78 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7018 (mt0) REVERT: A 130 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7941 (mm) REVERT: B 250 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7901 (tttp) REVERT: B 292 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6921 (p0) REVERT: L 49 ARG cc_start: 0.8033 (ttp-170) cc_final: 0.7358 (ttp-110) REVERT: L 95 ASP cc_start: 0.7985 (m-30) cc_final: 0.7365 (m-30) REVERT: L 130 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7905 (mt-10) REVERT: H 252 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8603 (mt-10) REVERT: K 4 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6082 (pp) REVERT: K 30 SER cc_start: 0.8450 (t) cc_final: 0.8196 (m) REVERT: K 34 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8654 (mmm) REVERT: K 44 GLU cc_start: 0.8770 (pm20) cc_final: 0.8264 (pm20) REVERT: K 88 PRO cc_start: 0.9093 (Cg_exo) cc_final: 0.8777 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8312 (pm20) cc_final: 0.7931 (pm20) REVERT: K 101 ASP cc_start: 0.8427 (t0) cc_final: 0.7935 (t0) outliers start: 22 outliers final: 12 residues processed: 117 average time/residue: 1.2295 time to fit residues: 151.3256 Evaluate side-chains 118 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 B residue 292 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU 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 34 MET 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: 1.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7720 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6785 Z= 0.242 Angle : 0.867 31.743 9231 Z= 0.354 Chirality : 0.042 0.146 1056 Planarity : 0.004 0.044 1153 Dihedral : 7.210 92.291 1052 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.63 % Allowed : 23.13 % Favored : 74.24 % 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: 1.41 (0.30), residues: 853 helix: 2.65 (0.44), residues: 141 sheet: 0.77 (0.28), residues: 347 loop : 0.54 (0.36), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 18 HIS 0.001 0.000 HIS B 241 PHE 0.011 0.001 PHE B 261 TYR 0.016 0.001 TYR K 60 ARG 0.003 0.000 ARG K 31 ********************** 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 119 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.9061 (ptp) cc_final: 0.8664 (ptt) REVERT: A 75 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6817 (tm-30) REVERT: A 78 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7032 (mt0) REVERT: A 130 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7961 (mm) REVERT: A 131 MET cc_start: 0.8402 (ttp) cc_final: 0.8193 (ttp) REVERT: B 250 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7898 (tttp) REVERT: B 292 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6919 (p0) REVERT: L 49 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7362 (ttp-110) REVERT: L 95 ASP cc_start: 0.7895 (m-30) cc_final: 0.7317 (m-30) REVERT: L 130 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7885 (mt-10) REVERT: H 252 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8584 (mt-10) REVERT: K 4 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6061 (pp) REVERT: K 30 SER cc_start: 0.8462 (t) cc_final: 0.8199 (m) REVERT: K 34 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8651 (mmm) REVERT: K 44 GLU cc_start: 0.8784 (pm20) cc_final: 0.8278 (pm20) REVERT: K 88 PRO cc_start: 0.9094 (Cg_exo) cc_final: 0.8772 (Cg_endo) REVERT: K 89 GLU cc_start: 0.8332 (pm20) cc_final: 0.7963 (pm20) REVERT: K 101 ASP cc_start: 0.8497 (t0) cc_final: 0.8002 (t0) outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 1.2020 time to fit residues: 144.0288 Evaluate side-chains 116 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 235 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU 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 34 MET Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 83 MET 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: 0.9990 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.0470 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 overall best weight: 0.3478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.069259 restraints weight = 14304.563| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.37 r_work: 0.2642 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6785 Z= 0.164 Angle : 0.851 31.540 9231 Z= 0.344 Chirality : 0.041 0.147 1056 Planarity : 0.004 0.045 1153 Dihedral : 7.089 91.976 1052 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.63 % Allowed : 23.41 % Favored : 73.96 % 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: 1.38 (0.31), residues: 853 helix: 2.51 (0.45), residues: 144 sheet: 0.82 (0.29), residues: 342 loop : 0.48 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 PHE 0.008 0.001 PHE B 316 TYR 0.016 0.001 TYR K 60 ARG 0.002 0.000 ARG K 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.22 seconds wall clock time: 56 minutes 32.58 seconds (3392.58 seconds total)