Starting phenix.real_space_refine on Thu Nov 14 12:10:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/11_2024/8j2f_35948.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/11_2024/8j2f_35948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/11_2024/8j2f_35948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/11_2024/8j2f_35948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/11_2024/8j2f_35948.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/11_2024/8j2f_35948.cif" } resolution = 3.07 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= 0.004 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: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 34 5.16 5 C 4002 2.51 5 N 1052 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6164 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3060 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 1, 'C14': 1, 'HP6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 1, 'C14': 1, 'HP6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.54, per 1000 atoms: 0.90 Number of scatterers: 6164 At special positions: 0 Unit cell: (76.2034, 91.2766, 103.838, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 Mg 2 11.99 O 1074 8.00 N 1052 7.00 C 4002 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: 1.72 Conformation dependent library (CDL) restraints added in 921.1 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 45.1% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.504A pdb=" N PHE A 113 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 115 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.515A pdb=" N ASN A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 348 Processing helix chain 'A' and resid 353 through 401 Proline residue: A 360 - end of helix removed outlier: 3.641A pdb=" N ALA A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 41 Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.505A pdb=" N PHE B 113 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 115 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.515A pdb=" N ASN B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 348 Processing helix chain 'B' and resid 353 through 401 Proline residue: B 360 - end of helix removed outlier: 3.641A pdb=" N ALA B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 73 removed outlier: 4.279A pdb=" N LEU A 82 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU A 44 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG A 10 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 46 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 12 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLU A 48 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A 14 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 50 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N CYS A 16 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A 255 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 278 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP A 206 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N THR A 257 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS A 208 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 97 removed outlier: 3.606A pdb=" N GLU A 92 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA A 117 " --> pdb=" O HIS A 136 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS A 136 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 135 " --> pdb=" O CYS A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.280A pdb=" N LEU B 82 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU B 44 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG B 10 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 46 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE B 12 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLU B 48 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 14 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 50 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N CYS B 16 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B 255 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B 278 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 206 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N THR B 257 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS B 208 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 97 removed outlier: 3.606A pdb=" N GLU B 92 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA B 117 " --> pdb=" O HIS B 136 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS B 136 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 135 " --> pdb=" O CYS B 176 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1044 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: 2.05 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1937 1.34 - 1.45: 1006 1.45 - 1.57: 3341 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 6334 Sorted by residual: bond pdb=" C TYR B 103 " pdb=" N PRO B 104 " ideal model delta sigma weight residual 1.336 1.370 -0.035 1.23e-02 6.61e+03 8.00e+00 bond pdb=" C TYR A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 1.336 1.370 -0.035 1.23e-02 6.61e+03 7.87e+00 bond pdb=" C ASP A 262 " pdb=" N PRO A 263 " ideal model delta sigma weight residual 1.337 1.363 -0.026 9.80e-03 1.04e+04 7.11e+00 bond pdb=" C ASP B 262 " pdb=" N PRO B 263 " ideal model delta sigma weight residual 1.337 1.362 -0.025 9.80e-03 1.04e+04 6.77e+00 bond pdb=" C THR B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.332 1.361 -0.030 1.33e-02 5.65e+03 4.94e+00 ... (remaining 6329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 7907 2.09 - 4.18: 541 4.18 - 6.28: 100 6.28 - 8.37: 20 8.37 - 10.46: 14 Bond angle restraints: 8582 Sorted by residual: angle pdb=" N THR A 259 " pdb=" CA THR A 259 " pdb=" C THR A 259 " ideal model delta sigma weight residual 111.74 120.68 -8.94 1.35e+00 5.49e-01 4.39e+01 angle pdb=" N THR B 259 " pdb=" CA THR B 259 " pdb=" C THR B 259 " ideal model delta sigma weight residual 111.74 120.66 -8.92 1.35e+00 5.49e-01 4.37e+01 angle pdb=" C TYR B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.56 113.66 5.90 1.01e+00 9.80e-01 3.41e+01 angle pdb=" C TYR A 67 " pdb=" N PRO A 68 " pdb=" CA PRO A 68 " ideal model delta sigma weight residual 119.56 113.68 5.88 1.01e+00 9.80e-01 3.39e+01 angle pdb=" N ILE B 147 " pdb=" CA ILE B 147 " pdb=" C ILE B 147 " ideal model delta sigma weight residual 112.80 106.35 6.45 1.15e+00 7.56e-01 3.15e+01 ... (remaining 8577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.77: 3277 12.77 - 25.55: 277 25.55 - 38.32: 76 38.32 - 51.10: 18 51.10 - 63.87: 6 Dihedral angle restraints: 3654 sinusoidal: 1444 harmonic: 2210 Sorted by residual: dihedral pdb=" C THR A 258 " pdb=" N THR A 258 " pdb=" CA THR A 258 " pdb=" CB THR A 258 " ideal model delta harmonic sigma weight residual -122.00 -135.74 13.74 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C THR B 258 " pdb=" N THR B 258 " pdb=" CA THR B 258 " pdb=" CB THR B 258 " ideal model delta harmonic sigma weight residual -122.00 -135.73 13.73 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" N THR A 258 " pdb=" C THR A 258 " pdb=" CA THR A 258 " pdb=" CB THR A 258 " ideal model delta harmonic sigma weight residual 123.40 134.28 -10.88 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 3651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 722 0.096 - 0.193: 154 0.193 - 0.289: 32 0.289 - 0.386: 10 0.386 - 0.482: 2 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA THR A 258 " pdb=" N THR A 258 " pdb=" C THR A 258 " pdb=" CB THR A 258 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA THR B 258 " pdb=" N THR B 258 " pdb=" C THR B 258 " pdb=" CB THR B 258 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA HIS B 375 " pdb=" N HIS B 375 " pdb=" C HIS B 375 " pdb=" CB HIS B 375 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 917 not shown) Planarity restraints: 1082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 359 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 360 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 359 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 360 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 229 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO B 230 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " -0.023 5.00e-02 4.00e+02 ... (remaining 1079 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 2742 2.96 - 3.44: 5946 3.44 - 3.93: 10715 3.93 - 4.41: 12188 4.41 - 4.90: 19869 Nonbonded interactions: 51460 Sorted by model distance: nonbonded pdb=" OE2 GLU A 49 " pdb="MG MG A 501 " model vdw 2.473 2.170 nonbonded pdb=" OE2 GLU B 49 " pdb="MG MG B 502 " model vdw 2.473 2.170 nonbonded pdb=" N ILE B 147 " pdb=" N TYR B 148 " model vdw 2.517 2.560 nonbonded pdb=" N ILE A 147 " pdb=" N TYR A 148 " model vdw 2.517 2.560 nonbonded pdb=" O THR B 258 " pdb=" OG1 THR B 258 " model vdw 2.568 3.040 ... (remaining 51455 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 3 through 401) selection = (chain 'B' and resid 3 through 401) } 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 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: 0.460 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.160 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.005 0.035 6334 Z= 0.357 Angle : 1.212 10.460 8582 Z= 0.791 Chirality : 0.089 0.482 920 Planarity : 0.005 0.048 1082 Dihedral : 10.867 63.871 2242 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.63 % Allowed : 3.76 % Favored : 95.61 % Cbeta Deviations : 0.28 % 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: 3.43 (0.30), residues: 760 helix: 4.63 (0.25), residues: 318 sheet: 2.15 (0.36), residues: 174 loop : -0.81 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 310 HIS 0.007 0.001 HIS A 109 PHE 0.015 0.002 PHE B 371 TYR 0.013 0.002 TYR B 105 ARG 0.004 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 383 TYR cc_start: 0.7201 (t80) cc_final: 0.6796 (t80) REVERT: B 92 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 106 MET cc_start: 0.8874 (mmm) cc_final: 0.8563 (mmt) REVERT: B 223 VAL cc_start: 0.8039 (t) cc_final: 0.7754 (t) REVERT: B 238 ASP cc_start: 0.7996 (m-30) cc_final: 0.7501 (m-30) REVERT: B 253 LYS cc_start: 0.7515 (tptt) cc_final: 0.7122 (tttm) REVERT: B 337 LEU cc_start: 0.8083 (tp) cc_final: 0.7878 (mm) outliers start: 4 outliers final: 0 residues processed: 146 average time/residue: 0.2779 time to fit residues: 49.5161 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 108 HIS A 136 HIS A 182 HIS A 272 HIS A 319 GLN A 400 GLN B 72 HIS B 108 HIS B 136 HIS B 182 HIS B 272 HIS B 319 GLN B 400 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 6334 Z= 0.381 Angle : 0.633 8.404 8582 Z= 0.336 Chirality : 0.046 0.187 920 Planarity : 0.005 0.036 1082 Dihedral : 5.996 46.449 862 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.88 % Allowed : 8.31 % Favored : 89.81 % 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: 2.75 (0.31), residues: 760 helix: 3.96 (0.27), residues: 320 sheet: 1.65 (0.35), residues: 174 loop : -0.93 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 17 HIS 0.008 0.001 HIS B 198 PHE 0.022 0.002 PHE B 371 TYR 0.011 0.002 TYR A 105 ARG 0.006 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7256 (ttpp) REVERT: A 253 LYS cc_start: 0.7688 (tptt) cc_final: 0.7325 (tttm) REVERT: A 383 TYR cc_start: 0.7668 (t80) cc_final: 0.7424 (t80) REVERT: B 184 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: B 253 LYS cc_start: 0.7653 (tptt) cc_final: 0.7254 (tttm) REVERT: B 383 TYR cc_start: 0.7637 (t80) cc_final: 0.7429 (t80) outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 0.2532 time to fit residues: 29.5513 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8374 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6334 Z= 0.148 Angle : 0.462 5.216 8582 Z= 0.250 Chirality : 0.039 0.145 920 Planarity : 0.003 0.032 1082 Dihedral : 5.331 51.543 862 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.78 % Allowed : 9.87 % Favored : 89.34 % 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: 3.13 (0.31), residues: 760 helix: 4.40 (0.27), residues: 318 sheet: 1.52 (0.35), residues: 174 loop : -0.61 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS A 375 PHE 0.011 0.001 PHE A 371 TYR 0.007 0.001 TYR A 105 ARG 0.003 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7061 (tptp) REVERT: B 30 MET cc_start: 0.8086 (mmt) cc_final: 0.7832 (mmp) REVERT: B 184 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7522 (pm20) outliers start: 5 outliers final: 1 residues processed: 88 average time/residue: 0.2049 time to fit residues: 23.2386 Evaluate side-chains 76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 6334 Z= 0.412 Angle : 0.596 9.017 8582 Z= 0.312 Chirality : 0.044 0.142 920 Planarity : 0.004 0.041 1082 Dihedral : 5.883 46.724 862 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.72 % Allowed : 11.13 % Favored : 87.15 % 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: 2.52 (0.31), residues: 760 helix: 3.72 (0.28), residues: 322 sheet: 1.29 (0.36), residues: 174 loop : -0.83 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 17 HIS 0.007 0.002 HIS A 198 PHE 0.017 0.002 PHE A 371 TYR 0.009 0.001 TYR A 98 ARG 0.003 0.001 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7168 (tptp) REVERT: B 30 MET cc_start: 0.8223 (mmt) cc_final: 0.7995 (mmp) REVERT: B 212 GLU cc_start: 0.7847 (mt-10) cc_final: 0.6947 (tm-30) REVERT: B 253 LYS cc_start: 0.7787 (tptt) cc_final: 0.7331 (tttm) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.2716 time to fit residues: 28.2175 Evaluate side-chains 81 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 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 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6334 Z= 0.159 Angle : 0.468 8.864 8582 Z= 0.245 Chirality : 0.039 0.136 920 Planarity : 0.003 0.034 1082 Dihedral : 5.330 52.296 862 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.88 % Allowed : 11.29 % Favored : 86.83 % 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: 2.83 (0.31), residues: 760 helix: 4.17 (0.27), residues: 318 sheet: 1.21 (0.36), residues: 174 loop : -0.65 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS B 375 PHE 0.012 0.001 PHE B 371 TYR 0.006 0.001 TYR A 105 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7204 (tptp) outliers start: 12 outliers final: 6 residues processed: 85 average time/residue: 0.2333 time to fit residues: 25.2517 Evaluate side-chains 78 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 6334 Z= 0.254 Angle : 0.504 6.836 8582 Z= 0.263 Chirality : 0.040 0.137 920 Planarity : 0.003 0.038 1082 Dihedral : 5.501 50.670 862 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.51 % Allowed : 11.13 % Favored : 86.36 % 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: 2.71 (0.32), residues: 760 helix: 4.05 (0.27), residues: 318 sheet: 1.13 (0.36), residues: 174 loop : -0.68 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS B 72 PHE 0.015 0.001 PHE A 371 TYR 0.006 0.001 TYR A 105 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7217 (tptp) REVERT: A 307 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7451 (ttmt) outliers start: 16 outliers final: 7 residues processed: 78 average time/residue: 0.2575 time to fit residues: 25.1332 Evaluate side-chains 74 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 6334 Z= 0.164 Angle : 0.453 5.370 8582 Z= 0.238 Chirality : 0.039 0.135 920 Planarity : 0.003 0.035 1082 Dihedral : 5.271 53.734 862 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.04 % Allowed : 11.76 % Favored : 86.21 % 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: 2.72 (0.32), residues: 760 helix: 4.07 (0.28), residues: 322 sheet: 1.11 (0.36), residues: 174 loop : -0.76 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.005 0.001 HIS B 375 PHE 0.013 0.001 PHE B 371 TYR 0.005 0.001 TYR A 105 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7295 (tptp) REVERT: A 307 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7440 (ttmt) outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 0.2361 time to fit residues: 24.6345 Evaluate side-chains 74 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 169 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 6334 Z= 0.365 Angle : 0.558 8.027 8582 Z= 0.290 Chirality : 0.042 0.139 920 Planarity : 0.004 0.043 1082 Dihedral : 5.688 48.293 862 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.04 % Allowed : 11.91 % Favored : 86.05 % 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: 2.38 (0.31), residues: 760 helix: 3.71 (0.28), residues: 322 sheet: 1.03 (0.36), residues: 174 loop : -0.88 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 17 HIS 0.005 0.001 HIS A 198 PHE 0.017 0.002 PHE A 371 TYR 0.006 0.001 TYR B 383 ARG 0.003 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7340 (tptp) REVERT: A 307 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7397 (ttmt) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 0.2566 time to fit residues: 25.2792 Evaluate side-chains 78 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 146 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 6334 Z= 0.299 Angle : 0.521 7.056 8582 Z= 0.271 Chirality : 0.041 0.139 920 Planarity : 0.004 0.043 1082 Dihedral : 5.574 48.565 862 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.04 % Allowed : 12.07 % Favored : 85.89 % 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: 2.45 (0.31), residues: 760 helix: 3.91 (0.27), residues: 318 sheet: 0.94 (0.36), residues: 174 loop : -0.88 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS B 72 PHE 0.015 0.001 PHE B 371 TYR 0.005 0.001 TYR A 141 ARG 0.002 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7340 (tptp) REVERT: A 307 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7409 (ttmt) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.2545 time to fit residues: 24.6555 Evaluate side-chains 78 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6334 Z= 0.152 Angle : 0.458 8.464 8582 Z= 0.237 Chirality : 0.038 0.134 920 Planarity : 0.003 0.036 1082 Dihedral : 5.203 54.380 862 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.72 % Allowed : 12.38 % Favored : 85.89 % 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: 2.67 (0.32), residues: 760 helix: 4.20 (0.28), residues: 318 sheet: 0.96 (0.36), residues: 174 loop : -0.84 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.005 0.001 HIS A 375 PHE 0.013 0.001 PHE B 371 TYR 0.004 0.001 TYR A 383 ARG 0.002 0.000 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7440 (tptp) REVERT: A 307 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7430 (ttmt) outliers start: 11 outliers final: 7 residues processed: 77 average time/residue: 0.2460 time to fit residues: 24.0037 Evaluate side-chains 76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.083923 restraints weight = 6828.289| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.13 r_work: 0.2649 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6334 Z= 0.285 Angle : 0.531 8.682 8582 Z= 0.271 Chirality : 0.041 0.136 920 Planarity : 0.003 0.039 1082 Dihedral : 5.462 48.683 862 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.72 % Allowed : 12.54 % Favored : 85.74 % 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: 2.50 (0.31), residues: 760 helix: 3.99 (0.28), residues: 318 sheet: 0.94 (0.36), residues: 174 loop : -0.88 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 310 HIS 0.005 0.001 HIS A 375 PHE 0.012 0.001 PHE A 371 TYR 0.005 0.001 TYR A 105 ARG 0.002 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.27 seconds wall clock time: 38 minutes 47.57 seconds (2327.57 seconds total)