Starting phenix.real_space_refine on Mon Sep 23 23:10:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/09_2024/7p8v_13255.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/09_2024/7p8v_13255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/09_2024/7p8v_13255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/09_2024/7p8v_13255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/09_2024/7p8v_13255.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/09_2024/7p8v_13255.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 2 5.21 5 S 16 5.16 5 C 3625 2.51 5 N 1108 2.21 5 O 1196 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-5461/modules/chem_data/mon_lib" Total number of atoms: 5988 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2601 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2601 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain: "C" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 458 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.35, per 1000 atoms: 0.73 Number of scatterers: 5988 At special positions: 0 Unit cell: (81.605, 73.015, 109.093, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 P 41 15.00 Mg 2 11.99 O 1196 8.00 N 1108 7.00 C 3625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 784.7 milliseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 39.9% alpha, 21.1% beta 12 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.748A pdb=" N GLU A 18 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 38 Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.754A pdb=" N LEU A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.126A pdb=" N ALA A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.620A pdb=" N LYS A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 182 removed outlier: 4.029A pdb=" N GLU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 223 removed outlier: 7.471A pdb=" N THR A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ALA A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.780A pdb=" N GLU B 18 " --> pdb=" O ILE B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 64 through 73 removed outlier: 4.151A pdb=" N ALA B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.632A pdb=" N ILE B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 163 through 182 Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.514A pdb=" N LEU B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 314 through 330 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137 removed outlier: 3.726A pdb=" N ALA A 120 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 125 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 108 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 148 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 146 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 191 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 231 removed outlier: 3.671A pdb=" N GLY A 238 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR A 255 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 292 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR A 257 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 113 removed outlier: 3.633A pdb=" N ARG B 55 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 197 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N HIS B 191 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 126 removed outlier: 3.644A pdb=" N ALA B 120 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 230 removed outlier: 3.714A pdb=" N GLY B 238 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 255 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU B 292 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR B 257 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS B 256 " --> pdb=" O MET B 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 299 through 300 262 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 951 1.31 - 1.44: 1701 1.44 - 1.56: 3415 1.56 - 1.69: 78 1.69 - 1.82: 24 Bond restraints: 6169 Sorted by residual: bond pdb=" N3B ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" N3B ANP B 702 " pdb=" PG ANP B 702 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" O3A ANP B 702 " pdb=" PB ANP B 702 " ideal model delta sigma weight residual 1.700 1.579 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" O3A ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 1.700 1.589 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3G ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.528 1.424 0.104 2.00e-02 2.50e+03 2.73e+01 ... (remaining 6164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 7056 2.56 - 5.12: 1429 5.12 - 7.68: 34 7.68 - 10.24: 3 10.24 - 12.80: 3 Bond angle restraints: 8525 Sorted by residual: angle pdb=" CA GLY B 127 " pdb=" C GLY B 127 " pdb=" O GLY B 127 " ideal model delta sigma weight residual 122.52 117.40 5.12 7.90e-01 1.60e+00 4.19e+01 angle pdb=" C GLN A 117 " pdb=" CA GLN A 117 " pdb=" CB GLN A 117 " ideal model delta sigma weight residual 109.54 120.67 -11.13 1.84e+00 2.95e-01 3.66e+01 angle pdb=" CA GLY A 127 " pdb=" C GLY A 127 " pdb=" O GLY A 127 " ideal model delta sigma weight residual 122.52 118.13 4.39 7.90e-01 1.60e+00 3.09e+01 angle pdb=" CA GLY A 217 " pdb=" C GLY A 217 " pdb=" O GLY A 217 " ideal model delta sigma weight residual 122.39 117.41 4.98 9.30e-01 1.16e+00 2.87e+01 angle pdb=" CA PRO A 7 " pdb=" C PRO A 7 " pdb=" O PRO A 7 " ideal model delta sigma weight residual 120.90 117.14 3.76 7.20e-01 1.93e+00 2.73e+01 ... (remaining 8520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 3336 29.54 - 59.07: 312 59.07 - 88.60: 19 88.60 - 118.14: 1 118.14 - 147.67: 2 Dihedral angle restraints: 3670 sinusoidal: 1752 harmonic: 1918 Sorted by residual: dihedral pdb=" C GLN A 117 " pdb=" N GLN A 117 " pdb=" CA GLN A 117 " pdb=" CB GLN A 117 " ideal model delta harmonic sigma weight residual -122.60 -134.60 12.00 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" O1B ANP A 701 " pdb=" N3B ANP A 701 " pdb=" PB ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sinusoidal sigma weight residual 35.15 -177.18 -147.67 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" O1A ANP B 702 " pdb=" O3A ANP B 702 " pdb=" PA ANP B 702 " pdb=" PB ANP B 702 " ideal model delta sinusoidal sigma weight residual 83.11 -46.03 129.14 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 3667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 354 0.061 - 0.121: 368 0.121 - 0.182: 186 0.182 - 0.242: 52 0.242 - 0.303: 6 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA GLN A 117 " pdb=" N GLN A 117 " pdb=" C GLN A 117 " pdb=" CB GLN A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA LEU B 234 " pdb=" N LEU B 234 " pdb=" C LEU B 234 " pdb=" CB LEU B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C3' ANP A 701 " pdb=" C2' ANP A 701 " pdb=" C4' ANP A 701 " pdb=" O3' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 963 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 208 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C LYS A 208 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS A 208 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU A 209 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 163 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C THR A 163 " 0.055 2.00e-02 2.50e+03 pdb=" O THR A 163 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 185 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C VAL B 185 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B 185 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 186 " 0.018 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 829 2.81 - 3.33: 5816 3.33 - 3.85: 9502 3.85 - 4.38: 12614 4.38 - 4.90: 19284 Nonbonded interactions: 48045 Sorted by model distance: nonbonded pdb=" OD1 ASN A 33 " pdb="MG MG A 702 " model vdw 2.287 2.170 nonbonded pdb="MG MG B 701 " pdb=" O2B ANP B 702 " model vdw 2.320 2.170 nonbonded pdb=" OD1 ASN B 33 " pdb="MG MG B 701 " model vdw 2.337 2.170 nonbonded pdb=" O3G ANP A 701 " pdb="MG MG A 702 " model vdw 2.341 2.170 nonbonded pdb=" O1A ANP A 701 " pdb="MG MG A 702 " model vdw 2.374 2.170 ... (remaining 48040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 331) selection = (chain 'B' and resid 1 through 331) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.280 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.175 6169 Z= 0.866 Angle : 1.812 12.797 8525 Z= 1.349 Chirality : 0.102 0.303 966 Planarity : 0.009 0.040 983 Dihedral : 20.306 147.672 2426 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.36 % Allowed : 7.85 % Favored : 91.79 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.31), residues: 658 helix: 1.02 (0.32), residues: 250 sheet: -0.83 (0.39), residues: 150 loop : -1.15 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 229 HIS 0.011 0.003 HIS B 170 PHE 0.031 0.005 PHE A 168 TYR 0.017 0.004 TYR A 257 ARG 0.013 0.002 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 143 THR cc_start: 0.9100 (m) cc_final: 0.8816 (p) REVERT: A 169 ASN cc_start: 0.8237 (m110) cc_final: 0.7878 (m110) REVERT: A 173 GLU cc_start: 0.7886 (tp30) cc_final: 0.7613 (tp30) REVERT: A 229 TRP cc_start: 0.8208 (t-100) cc_final: 0.7829 (t-100) REVERT: A 231 HIS cc_start: 0.6665 (t70) cc_final: 0.6349 (t70) REVERT: B 22 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7729 (mtm-85) REVERT: B 274 GLN cc_start: 0.7801 (mt0) cc_final: 0.7304 (tt0) outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.1998 time to fit residues: 20.2276 Evaluate side-chains 51 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 188 ASN B 122 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6169 Z= 0.224 Angle : 0.596 7.336 8525 Z= 0.326 Chirality : 0.043 0.158 966 Planarity : 0.005 0.045 983 Dihedral : 21.062 142.534 1176 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.82 % Allowed : 12.96 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.33), residues: 658 helix: 1.22 (0.32), residues: 256 sheet: -0.56 (0.39), residues: 172 loop : -0.85 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.004 0.001 HIS B 170 PHE 0.015 0.002 PHE A 183 TYR 0.010 0.002 TYR B 124 ARG 0.005 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7853 (tp30) cc_final: 0.7378 (tt0) REVERT: B 274 GLN cc_start: 0.8184 (mt0) cc_final: 0.7923 (mp10) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.1541 time to fit residues: 14.6242 Evaluate side-chains 48 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6169 Z= 0.176 Angle : 0.527 6.501 8525 Z= 0.289 Chirality : 0.041 0.148 966 Planarity : 0.004 0.039 983 Dihedral : 20.746 135.984 1172 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.19 % Allowed : 15.15 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.33), residues: 658 helix: 0.93 (0.32), residues: 270 sheet: -0.37 (0.40), residues: 160 loop : -1.13 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 229 HIS 0.009 0.001 HIS B 308 PHE 0.013 0.001 PHE A 168 TYR 0.008 0.001 TYR B 257 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8001 (tp30) cc_final: 0.7723 (tp30) REVERT: A 293 GLU cc_start: 0.7777 (tp30) cc_final: 0.7399 (tt0) REVERT: B 128 ARG cc_start: 0.8388 (tpm170) cc_final: 0.8152 (tpm170) REVERT: B 274 GLN cc_start: 0.8105 (mt0) cc_final: 0.7883 (mt0) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 0.1984 time to fit residues: 15.7868 Evaluate side-chains 52 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6169 Z= 0.343 Angle : 0.596 6.213 8525 Z= 0.323 Chirality : 0.043 0.158 966 Planarity : 0.005 0.042 983 Dihedral : 20.813 144.690 1172 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.28 % Allowed : 15.88 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.33), residues: 658 helix: 0.78 (0.32), residues: 270 sheet: -0.79 (0.39), residues: 168 loop : -1.10 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.006 0.001 HIS B 75 PHE 0.029 0.003 PHE A 168 TYR 0.015 0.002 TYR B 291 ARG 0.005 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.623 Fit side-chains REVERT: A 173 GLU cc_start: 0.8207 (tp30) cc_final: 0.7893 (tp30) REVERT: A 293 GLU cc_start: 0.7805 (tp30) cc_final: 0.7342 (tt0) REVERT: B 128 ARG cc_start: 0.8502 (tpm170) cc_final: 0.8222 (tpm170) REVERT: B 274 GLN cc_start: 0.8151 (mt0) cc_final: 0.7921 (mt0) outliers start: 18 outliers final: 14 residues processed: 61 average time/residue: 0.1712 time to fit residues: 14.9630 Evaluate side-chains 54 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6169 Z= 0.410 Angle : 0.623 6.107 8525 Z= 0.337 Chirality : 0.045 0.158 966 Planarity : 0.005 0.045 983 Dihedral : 20.863 150.632 1172 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.29 % Allowed : 16.24 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.34), residues: 658 helix: 0.91 (0.33), residues: 256 sheet: -0.93 (0.38), residues: 180 loop : -1.02 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 229 HIS 0.006 0.001 HIS B 304 PHE 0.026 0.003 PHE A 168 TYR 0.021 0.002 TYR B 257 ARG 0.004 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 47 time to evaluate : 0.623 Fit side-chains REVERT: A 162 ARG cc_start: 0.8670 (mmp-170) cc_final: 0.8426 (mmp-170) REVERT: A 173 GLU cc_start: 0.8151 (tp30) cc_final: 0.7805 (tp30) REVERT: B 128 ARG cc_start: 0.8563 (tpm170) cc_final: 0.8302 (tpm170) REVERT: B 161 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 223 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7271 (mp-120) REVERT: B 274 GLN cc_start: 0.8170 (mt0) cc_final: 0.7937 (mt0) outliers start: 29 outliers final: 18 residues processed: 70 average time/residue: 0.1977 time to fit residues: 18.0957 Evaluate side-chains 64 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6169 Z= 0.199 Angle : 0.524 5.863 8525 Z= 0.285 Chirality : 0.041 0.149 966 Planarity : 0.004 0.044 983 Dihedral : 20.567 148.625 1172 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.47 % Allowed : 17.34 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.34), residues: 658 helix: 0.61 (0.32), residues: 272 sheet: -0.75 (0.40), residues: 168 loop : -1.09 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.004 0.001 HIS B 308 PHE 0.015 0.002 PHE A 168 TYR 0.009 0.001 TYR B 257 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.646 Fit side-chains REVERT: A 173 GLU cc_start: 0.7956 (tp30) cc_final: 0.7597 (tp30) REVERT: B 128 ARG cc_start: 0.8528 (tpm170) cc_final: 0.8281 (tpm170) REVERT: B 161 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8333 (mp) REVERT: B 274 GLN cc_start: 0.8160 (mt0) cc_final: 0.7915 (mt0) outliers start: 19 outliers final: 14 residues processed: 61 average time/residue: 0.1971 time to fit residues: 15.9807 Evaluate side-chains 57 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6169 Z= 0.195 Angle : 0.517 7.310 8525 Z= 0.277 Chirality : 0.040 0.147 966 Planarity : 0.004 0.045 983 Dihedral : 20.337 147.723 1172 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.65 % Allowed : 17.88 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.34), residues: 658 helix: 0.68 (0.32), residues: 272 sheet: -0.62 (0.41), residues: 168 loop : -1.02 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS B 308 PHE 0.014 0.002 PHE A 168 TYR 0.009 0.001 TYR B 257 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 0.554 Fit side-chains REVERT: A 173 GLU cc_start: 0.7923 (tp30) cc_final: 0.7680 (tp30) REVERT: A 293 GLU cc_start: 0.7863 (tp30) cc_final: 0.7348 (tt0) REVERT: B 128 ARG cc_start: 0.8544 (tpm170) cc_final: 0.8279 (tpm170) REVERT: B 161 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 274 GLN cc_start: 0.8104 (mt0) cc_final: 0.7854 (mt0) outliers start: 20 outliers final: 15 residues processed: 58 average time/residue: 0.2091 time to fit residues: 15.8129 Evaluate side-chains 56 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6169 Z= 0.182 Angle : 0.506 8.219 8525 Z= 0.272 Chirality : 0.040 0.144 966 Planarity : 0.004 0.045 983 Dihedral : 20.226 149.608 1172 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.10 % Allowed : 18.61 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.34), residues: 658 helix: 0.75 (0.33), residues: 272 sheet: -0.57 (0.41), residues: 168 loop : -0.97 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 308 PHE 0.012 0.002 PHE A 168 TYR 0.008 0.001 TYR B 257 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.542 Fit side-chains REVERT: A 173 GLU cc_start: 0.7906 (tp30) cc_final: 0.7653 (tp30) REVERT: B 128 ARG cc_start: 0.8552 (tpm170) cc_final: 0.8283 (tpm170) REVERT: B 274 GLN cc_start: 0.8069 (mt0) cc_final: 0.7811 (mt0) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.2019 time to fit residues: 14.7079 Evaluate side-chains 53 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 6169 Z= 0.493 Angle : 0.671 10.137 8525 Z= 0.360 Chirality : 0.047 0.163 966 Planarity : 0.005 0.046 983 Dihedral : 20.568 154.215 1172 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.93 % Allowed : 17.34 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.34), residues: 658 helix: 0.45 (0.32), residues: 270 sheet: -0.85 (0.39), residues: 170 loop : -1.15 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 229 HIS 0.006 0.002 HIS B 304 PHE 0.033 0.003 PHE A 168 TYR 0.020 0.003 TYR B 291 ARG 0.004 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 46 time to evaluate : 0.596 Fit side-chains REVERT: A 173 GLU cc_start: 0.8244 (tp30) cc_final: 0.7894 (tp30) REVERT: A 176 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8508 (ptp-110) REVERT: A 293 GLU cc_start: 0.7930 (tp30) cc_final: 0.7397 (tt0) REVERT: B 22 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7545 (mtm-85) REVERT: B 128 ARG cc_start: 0.8592 (tpm170) cc_final: 0.8278 (tpm170) REVERT: B 274 GLN cc_start: 0.8184 (mt0) cc_final: 0.7919 (mt0) outliers start: 27 outliers final: 22 residues processed: 64 average time/residue: 0.2136 time to fit residues: 17.8955 Evaluate side-chains 68 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 44 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6169 Z= 0.185 Angle : 0.535 11.542 8525 Z= 0.289 Chirality : 0.041 0.150 966 Planarity : 0.004 0.043 983 Dihedral : 20.293 148.438 1172 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.28 % Allowed : 19.34 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.34), residues: 658 helix: 0.62 (0.33), residues: 272 sheet: -0.70 (0.40), residues: 170 loop : -1.07 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 121 HIS 0.004 0.001 HIS B 308 PHE 0.010 0.001 PHE A 160 TYR 0.008 0.001 TYR B 257 ARG 0.003 0.000 ARG A 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.626 Fit side-chains REVERT: A 173 GLU cc_start: 0.7937 (tp30) cc_final: 0.7574 (tp30) REVERT: A 176 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8447 (ptp-110) REVERT: A 293 GLU cc_start: 0.7894 (tp30) cc_final: 0.7388 (tt0) REVERT: B 128 ARG cc_start: 0.8539 (tpm170) cc_final: 0.8291 (tpm170) REVERT: B 274 GLN cc_start: 0.8097 (mt0) cc_final: 0.7843 (mt0) outliers start: 18 outliers final: 14 residues processed: 57 average time/residue: 0.2029 time to fit residues: 15.3713 Evaluate side-chains 55 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.088438 restraints weight = 10291.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091461 restraints weight = 5626.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093532 restraints weight = 3827.930| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6169 Z= 0.295 Angle : 0.577 10.502 8525 Z= 0.308 Chirality : 0.042 0.155 966 Planarity : 0.004 0.044 983 Dihedral : 20.261 149.539 1172 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.01 % Allowed : 18.98 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.34), residues: 658 helix: 0.59 (0.33), residues: 272 sheet: -0.69 (0.40), residues: 170 loop : -1.14 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.004 0.001 HIS B 304 PHE 0.023 0.003 PHE A 168 TYR 0.013 0.002 TYR B 257 ARG 0.003 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.06 seconds wall clock time: 26 minutes 1.71 seconds (1561.71 seconds total)