Starting phenix.real_space_refine on Wed Feb 12 01:48:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4v_41899/02_2025/8u4v_41899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4v_41899/02_2025/8u4v_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/cci-nas-00/data/ceres_data/8u4v_41899/02_2025/8u4v_41899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4v_41899/02_2025/8u4v_41899.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4v_41899/02_2025/8u4v_41899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4v_41899/02_2025/8u4v_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. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.21, per 1000 atoms: 0.78 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 1.1 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: 0.90 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: 2.01 Time building geometry restraints manager: 1.85 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: 0.00 - 6.71: 9215 6.71 - 13.42: 9 13.42 - 20.13: 2 20.13 - 26.84: 3 26.84 - 33.55: 2 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 3.040 nonbonded pdb=" OG SER L 51 " pdb=" OE1 GLN L 52 " model vdw 2.199 3.040 nonbonded pdb=" O ALA L 178 " pdb=" NE2 GLN L 180 " model vdw 2.287 3.120 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 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.700 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.150 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.623 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: 1.2398 time to fit residues: 193.6191 Evaluate side-chains 114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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: 0.0060 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN L 115 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.064239 restraints weight = 20684.991| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.85 r_work: 0.2529 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 6785 Z= 0.388 Angle : 0.935 32.206 9231 Z= 0.399 Chirality : 0.045 0.175 1056 Planarity : 0.004 0.051 1153 Dihedral : 8.898 88.673 1056 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.46 % Allowed : 20.36 % Favored : 76.18 % 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: 0.99 (0.30), residues: 853 helix: 2.30 (0.42), residues: 141 sheet: 0.46 (0.28), residues: 353 loop : 0.34 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 125 HIS 0.003 0.001 HIS H 127 PHE 0.017 0.002 PHE B 261 TYR 0.016 0.002 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 138 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.777 Fit side-chains REVERT: A 78 GLN cc_start: 0.8448 (tt0) cc_final: 0.8125 (mt0) REVERT: A 130 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8750 (mm) REVERT: B 250 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8733 (tttp) REVERT: L 49 ARG cc_start: 0.8919 (ttp-170) cc_final: 0.8481 (ttp-110) REVERT: L 91 ARG cc_start: 0.8978 (ttt180) cc_final: 0.8744 (ttt180) REVERT: L 95 ASP cc_start: 0.8889 (m-30) cc_final: 0.8267 (m-30) REVERT: L 130 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: L 175 VAL cc_start: 0.9220 (m) cc_final: 0.8889 (t) REVERT: H 178 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8777 (mp) REVERT: H 239 ASN cc_start: 0.9201 (t0) cc_final: 0.8891 (t0) REVERT: H 246 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8822 (mmmt) REVERT: K 89 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8156 (pm20) outliers start: 25 outliers final: 5 residues processed: 124 average time/residue: 1.3338 time to fit residues: 173.0991 Evaluate side-chains 110 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 246 LYS 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 82 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 185 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.065674 restraints weight = 16620.431| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.61 r_work: 0.2561 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2431 r_free = 0.2431 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2431 r_free = 0.2431 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6785 Z= 0.264 Angle : 0.886 32.393 9231 Z= 0.368 Chirality : 0.043 0.144 1056 Planarity : 0.004 0.058 1153 Dihedral : 7.437 89.882 1055 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.02 % Allowed : 21.05 % Favored : 74.93 % 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: 1.17 (0.30), residues: 853 helix: 2.46 (0.44), residues: 142 sheet: 0.59 (0.28), residues: 349 loop : 0.43 (0.36), residues: 362 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 0.012 0.001 PHE B 261 TYR 0.010 0.001 TYR B 264 ARG 0.003 0.000 ARG K 53 *********************** 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 to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.770 Fit side-chains REVERT: A 130 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8782 (mm) REVERT: B 250 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8737 (tttp) REVERT: L 49 ARG cc_start: 0.8991 (ttp-170) cc_final: 0.8495 (ttp-110) REVERT: L 95 ASP cc_start: 0.8957 (m-30) cc_final: 0.8247 (m-30) REVERT: L 130 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8436 (mt-10) REVERT: L 175 VAL cc_start: 0.9203 (m) cc_final: 0.9002 (t) REVERT: H 239 ASN cc_start: 0.9280 (t0) cc_final: 0.8977 (t0) REVERT: H 246 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8895 (mmmt) REVERT: K 4 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7780 (pp) REVERT: K 5 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8492 (tm-30) outliers start: 29 outliers final: 9 residues processed: 124 average time/residue: 1.3849 time to fit residues: 181.0142 Evaluate side-chains 115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 201 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.066055 restraints weight = 17302.062| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.67 r_work: 0.2572 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6785 Z= 0.232 Angle : 0.868 32.059 9231 Z= 0.359 Chirality : 0.042 0.145 1056 Planarity : 0.004 0.045 1153 Dihedral : 7.264 91.013 1052 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.16 % Allowed : 20.78 % Favored : 75.07 % 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: 1.35 (0.31), residues: 853 helix: 2.64 (0.44), residues: 141 sheet: 0.69 (0.28), residues: 347 loop : 0.54 (0.36), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.011 0.001 PHE B 261 TYR 0.013 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 140 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.906 Fit side-chains REVERT: A 78 GLN cc_start: 0.8472 (tt0) cc_final: 0.8096 (mt0) REVERT: A 130 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8804 (mm) REVERT: B 250 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8739 (tttp) REVERT: L 49 ARG cc_start: 0.9034 (ttp-170) cc_final: 0.8546 (ttp-110) REVERT: L 95 ASP cc_start: 0.8975 (m-30) cc_final: 0.8286 (m-30) REVERT: L 120 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8809 (mp) REVERT: H 239 ASN cc_start: 0.9288 (t0) cc_final: 0.8980 (t0) REVERT: H 246 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8907 (mmmt) REVERT: K 4 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7794 (pp) outliers start: 30 outliers final: 14 residues processed: 126 average time/residue: 1.2791 time to fit residues: 169.4509 Evaluate side-chains 121 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 L residue 238 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 201 SER 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 11 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.088065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.066938 restraints weight = 11541.523| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.10 r_work: 0.2597 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2332 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 : 0.884 32.022 9231 Z= 0.370 Chirality : 0.042 0.145 1056 Planarity : 0.004 0.040 1153 Dihedral : 7.300 91.847 1052 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.88 % Allowed : 21.33 % Favored : 74.79 % 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 (0.31), residues: 853 helix: 2.59 (0.44), residues: 141 sheet: 0.75 (0.29), residues: 337 loop : 0.44 (0.36), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.003 0.001 HIS H 127 PHE 0.013 0.001 PHE B 261 TYR 0.012 0.001 TYR K 104 ARG 0.003 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 134 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.690 Fit side-chains REVERT: A 78 GLN cc_start: 0.8530 (tt0) cc_final: 0.8197 (mt0) REVERT: A 130 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8790 (mm) REVERT: B 250 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8734 (tttp) REVERT: L 49 ARG cc_start: 0.8959 (ttp-170) cc_final: 0.8502 (ttp-110) REVERT: L 95 ASP cc_start: 0.8947 (m-30) cc_final: 0.8197 (m-30) REVERT: L 120 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8838 (mp) REVERT: L 190 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8479 (mm-30) REVERT: H 239 ASN cc_start: 0.9200 (t0) cc_final: 0.8900 (t0) REVERT: H 246 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8884 (mmmt) REVERT: K 4 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7840 (pp) REVERT: K 34 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8887 (mmm) outliers start: 28 outliers final: 16 residues processed: 121 average time/residue: 1.3222 time to fit residues: 167.7344 Evaluate side-chains 122 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 L residue 238 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 201 SER 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 11 LEU Chi-restraints excluded: chain K residue 34 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.089577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.065862 restraints weight = 20662.479| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.87 r_work: 0.2564 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6785 Z= 0.214 Angle : 0.867 31.709 9231 Z= 0.358 Chirality : 0.041 0.146 1056 Planarity : 0.004 0.039 1153 Dihedral : 7.230 91.928 1052 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.74 % Allowed : 21.61 % Favored : 74.65 % 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: 1.42 (0.31), residues: 853 helix: 2.69 (0.45), residues: 141 sheet: 0.81 (0.29), residues: 338 loop : 0.51 (0.36), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 18 HIS 0.002 0.000 HIS H 127 PHE 0.010 0.001 PHE B 261 TYR 0.009 0.001 TYR A 67 ARG 0.002 0.000 ARG K 53 *********************** 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 to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.740 Fit side-chains REVERT: A 78 GLN cc_start: 0.8428 (tt0) cc_final: 0.8085 (mt0) REVERT: A 130 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8715 (mm) REVERT: B 250 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8687 (tttp) REVERT: L 49 ARG cc_start: 0.8880 (ttp-170) cc_final: 0.8670 (ttp-170) REVERT: L 120 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8769 (mp) REVERT: H 239 ASN cc_start: 0.9123 (t0) cc_final: 0.8760 (t0) REVERT: K 4 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7789 (pp) REVERT: K 34 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8825 (mmm) outliers start: 27 outliers final: 12 residues processed: 123 average time/residue: 1.2836 time to fit residues: 165.6547 Evaluate side-chains 119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain B residue 254 LEU 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 38 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 83 MET 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 64 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.065846 restraints weight = 14153.769| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.39 r_work: 0.2571 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6785 Z= 0.295 Angle : 0.887 31.832 9231 Z= 0.371 Chirality : 0.042 0.147 1056 Planarity : 0.004 0.040 1153 Dihedral : 7.296 92.110 1052 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.60 % Allowed : 21.75 % Favored : 74.65 % 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: 2.60 (0.44), residues: 141 sheet: 0.80 (0.29), residues: 336 loop : 0.48 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 125 HIS 0.001 0.001 HIS L 223 PHE 0.014 0.001 PHE B 261 TYR 0.012 0.001 TYR K 104 ARG 0.003 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 125 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.748 Fit side-chains REVERT: A 61 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: A 78 GLN cc_start: 0.8529 (tt0) cc_final: 0.8194 (mt0) REVERT: A 130 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8800 (mm) REVERT: B 250 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8703 (tttp) REVERT: L 49 ARG cc_start: 0.9003 (ttp-170) cc_final: 0.8770 (ttp-170) REVERT: L 120 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8801 (mp) REVERT: H 239 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.8897 (t0) REVERT: K 4 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7853 (pp) REVERT: K 34 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8970 (mmm) outliers start: 26 outliers final: 13 residues processed: 114 average time/residue: 1.3176 time to fit residues: 157.4287 Evaluate side-chains 116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 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 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 109 MET Chi-restraints excluded: chain H residue 201 SER 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 34 MET Chi-restraints excluded: chain K residue 83 MET 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 61 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.065777 restraints weight = 14697.699| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.42 r_work: 0.2568 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2543 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= 0.280 Angle : 0.884 31.745 9231 Z= 0.369 Chirality : 0.042 0.147 1056 Planarity : 0.004 0.040 1153 Dihedral : 7.289 92.068 1052 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.60 % Allowed : 21.75 % Favored : 74.65 % 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: 1.39 (0.31), residues: 853 helix: 2.65 (0.44), residues: 141 sheet: 0.79 (0.29), residues: 337 loop : 0.50 (0.36), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 125 HIS 0.003 0.001 HIS H 240 PHE 0.013 0.001 PHE B 261 TYR 0.010 0.001 TYR A 67 ARG 0.002 0.000 ARG K 53 *********************** 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 127 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.702 Fit side-chains REVERT: A 61 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: A 75 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 78 GLN cc_start: 0.8555 (tt0) cc_final: 0.8235 (mt0) REVERT: A 130 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8814 (mm) REVERT: B 250 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8692 (tttp) REVERT: L 49 ARG cc_start: 0.9006 (ttp-170) cc_final: 0.8770 (ttp-170) REVERT: L 120 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8819 (mp) REVERT: H 239 ASN cc_start: 0.9319 (OUTLIER) cc_final: 0.9117 (t0) REVERT: K 4 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7918 (pp) outliers start: 26 outliers final: 14 residues processed: 115 average time/residue: 1.2599 time to fit residues: 152.1500 Evaluate side-chains 117 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 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 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 109 MET Chi-restraints excluded: chain H residue 201 SER 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 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 3 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.066110 restraints weight = 16650.926| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.60 r_work: 0.2575 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6785 Z= 0.221 Angle : 0.879 31.652 9231 Z= 0.365 Chirality : 0.042 0.147 1056 Planarity : 0.004 0.041 1153 Dihedral : 7.259 91.856 1052 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.77 % Allowed : 21.75 % 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: 1.43 (0.31), residues: 853 helix: 2.69 (0.45), residues: 141 sheet: 0.82 (0.29), residues: 336 loop : 0.52 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 18 HIS 0.002 0.001 HIS H 240 PHE 0.010 0.001 PHE B 261 TYR 0.011 0.001 TYR A 67 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 124 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.721 Fit side-chains REVERT: A 75 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7059 (tm-30) REVERT: A 78 GLN cc_start: 0.8518 (tt0) cc_final: 0.8197 (mt0) REVERT: A 130 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 250 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8733 (tttp) REVERT: L 49 ARG cc_start: 0.9018 (ttp-170) cc_final: 0.8780 (ttp-170) REVERT: L 120 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8809 (mp) REVERT: H 239 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.8813 (t0) REVERT: K 4 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7858 (pp) REVERT: K 89 GLU cc_start: 0.8971 (pm20) cc_final: 0.8715 (pm20) outliers start: 20 outliers final: 12 residues processed: 115 average time/residue: 1.2760 time to fit residues: 154.2472 Evaluate side-chains 118 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain B residue 254 LEU 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 38 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain K residue 4 LEU 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 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.0070 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 82 optimal weight: 0.0030 chunk 74 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.0670 chunk 35 optimal weight: 0.9980 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 239 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.090144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.066314 restraints weight = 22598.233| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.95 r_work: 0.2573 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2618 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= 0.179 Angle : 0.876 31.539 9231 Z= 0.364 Chirality : 0.042 0.147 1056 Planarity : 0.004 0.040 1153 Dihedral : 7.207 91.455 1052 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 22.58 % Favored : 75.07 % 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: 1.47 (0.31), residues: 853 helix: 2.73 (0.45), residues: 141 sheet: 0.89 (0.29), residues: 329 loop : 0.49 (0.35), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 18 HIS 0.005 0.001 HIS H 240 PHE 0.010 0.001 PHE B 316 TYR 0.012 0.001 TYR K 110 ARG 0.002 0.000 ARG K 53 ********************** 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 120 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.744 Fit side-chains REVERT: A 75 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7046 (tm-30) REVERT: A 78 GLN cc_start: 0.8449 (tt0) cc_final: 0.8168 (mt0) REVERT: A 130 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8670 (mm) REVERT: B 250 LYS cc_start: 0.9019 (ttpt) cc_final: 0.8713 (tttp) REVERT: L 49 ARG cc_start: 0.8908 (ttp-170) cc_final: 0.8696 (ttp-170) REVERT: L 120 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8771 (mp) REVERT: H 239 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8872 (t0) REVERT: K 4 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7851 (pp) REVERT: K 34 MET cc_start: 0.9040 (mmm) cc_final: 0.8840 (mmm) REVERT: K 62 ASP cc_start: 0.8664 (m-30) cc_final: 0.8415 (t0) outliers start: 17 outliers final: 11 residues processed: 114 average time/residue: 1.2734 time to fit residues: 152.3544 Evaluate side-chains 116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain B residue 254 LEU 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 38 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.067502 restraints weight = 14210.338| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.41 r_work: 0.2606 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6785 Z= 0.227 Angle : 0.883 31.545 9231 Z= 0.368 Chirality : 0.042 0.178 1056 Planarity : 0.004 0.040 1153 Dihedral : 7.198 91.276 1052 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.22 % Allowed : 22.85 % Favored : 74.93 % 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: 1.46 (0.31), residues: 853 helix: 2.72 (0.45), residues: 141 sheet: 0.91 (0.29), residues: 328 loop : 0.46 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 18 HIS 0.005 0.001 HIS H 240 PHE 0.010 0.001 PHE B 316 TYR 0.010 0.001 TYR A 67 ARG 0.002 0.000 ARG K 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5481.76 seconds wall clock time: 97 minutes 37.07 seconds (5857.07 seconds total)