Starting phenix.real_space_refine on Sun Mar 10 23:52:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/03_2024/8j2f_35948_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/03_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_35948/03_2024/8j2f_35948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/03_2024/8j2f_35948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/03_2024/8j2f_35948_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2f_35948/03_2024/8j2f_35948_updated.pdb" } 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 Residue "A GLU 256": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6164 Number of models: 1 Model: "" Number of chains: 4 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: "B" 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} Time building chain proxies: 3.93, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.3 seconds 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... running ksdssp... Secondary structure from input PDB file: 18 helices and 4 sheets defined 40.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 200 through 203 No H-bonds generated for 'chain 'A' and resid 200 through 203' Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 303 through 347 Processing helix chain 'A' and resid 354 through 400 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 26 through 40 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 186 through 195 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 303 through 347 Processing helix chain 'B' and resid 354 through 400 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= A, 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: 3.839A pdb=" N LEU A 14 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 254 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE A 280 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N CYS A 252 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ARG A 282 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE A 250 " --> pdb=" O ARG A 282 " (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= B, 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: 6.649A pdb=" N VAL A 172 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TYR A 133 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 174 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR A 135 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N CYS A 176 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id= C, 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: 3.838A pdb=" N LEU B 14 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 254 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE B 280 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N CYS B 252 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ARG B 282 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE B 250 " --> pdb=" O ARG B 282 " (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= D, 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: 6.648A pdb=" N VAL B 172 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR B 133 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 174 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR B 135 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N CYS B 176 " --> pdb=" O THR B 135 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 2.50 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: 99.48 - 106.67: 208 106.67 - 113.87: 3425 113.87 - 121.07: 3543 121.07 - 128.26: 1310 128.26 - 135.46: 96 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: 2760 2.96 - 3.44: 5970 3.44 - 3.93: 10769 3.93 - 4.41: 12246 4.41 - 4.90: 19875 Nonbonded interactions: 51620 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 2.440 ... (remaining 51615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.470 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: 2.600 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.950 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- 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= 0.356 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 fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 0.699 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: 0.2595 time to fit residues: 46.2146 Evaluate side-chains 83 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6334 Z= 0.337 Angle : 0.575 8.121 8582 Z= 0.306 Chirality : 0.044 0.186 920 Planarity : 0.004 0.037 1082 Dihedral : 5.656 43.810 862 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.04 % Allowed : 8.31 % Favored : 89.66 % 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: 2.91 (0.31), residues: 760 helix: 4.18 (0.27), residues: 318 sheet: 1.72 (0.35), residues: 174 loop : -0.93 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 17 HIS 0.008 0.001 HIS A 198 PHE 0.019 0.002 PHE B 371 TYR 0.014 0.001 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 87 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.652 Fit side-chains REVERT: A 52 SER cc_start: 0.8875 (t) cc_final: 0.8605 (m) REVERT: A 145 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7269 (ttpp) REVERT: A 383 TYR cc_start: 0.7590 (t80) cc_final: 0.7370 (t80) REVERT: B 184 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: B 253 LYS cc_start: 0.7616 (tptt) cc_final: 0.7244 (tttm) REVERT: B 383 TYR cc_start: 0.7558 (t80) cc_final: 0.7326 (t80) outliers start: 13 outliers final: 5 residues processed: 86 average time/residue: 0.2620 time to fit residues: 28.2361 Evaluate side-chains 78 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 B residue 41 SER 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: 6.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6334 Z= 0.290 Angle : 0.521 7.463 8582 Z= 0.277 Chirality : 0.041 0.146 920 Planarity : 0.004 0.033 1082 Dihedral : 5.582 48.719 862 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.35 % Allowed : 9.72 % Favored : 87.93 % 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: 2.76 (0.31), residues: 760 helix: 3.93 (0.27), residues: 320 sheet: 1.48 (0.36), residues: 174 loop : -0.71 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.005 0.001 HIS B 72 PHE 0.014 0.001 PHE A 371 TYR 0.009 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 95 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 52 SER cc_start: 0.8934 (t) cc_final: 0.8693 (m) REVERT: A 253 LYS cc_start: 0.7754 (tptt) cc_final: 0.7329 (tttm) REVERT: B 30 MET cc_start: 0.8179 (mmt) cc_final: 0.7862 (mmp) REVERT: B 184 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: B 253 LYS cc_start: 0.7743 (tptt) cc_final: 0.7309 (tttm) REVERT: B 337 LEU cc_start: 0.8104 (tp) cc_final: 0.7866 (tt) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.2356 time to fit residues: 26.8309 Evaluate side-chains 85 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 147 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 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 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 6334 Z= 0.375 Angle : 0.549 7.868 8582 Z= 0.288 Chirality : 0.042 0.137 920 Planarity : 0.004 0.037 1082 Dihedral : 5.725 46.999 862 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.35 % Allowed : 11.44 % 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: 2.37 (0.31), residues: 760 helix: 3.66 (0.28), residues: 318 sheet: 1.20 (0.36), residues: 174 loop : -0.90 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 17 HIS 0.006 0.001 HIS A 72 PHE 0.016 0.002 PHE A 371 TYR 0.009 0.001 TYR A 105 ARG 0.003 0.000 ARG B 397 *********************** 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 87 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.738 Fit side-chains REVERT: A 43 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8397 (t0) REVERT: A 52 SER cc_start: 0.8907 (t) cc_final: 0.8692 (m) REVERT: A 145 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7212 (tptp) REVERT: B 24 LYS cc_start: 0.8546 (mttm) cc_final: 0.8158 (mttp) REVERT: B 30 MET cc_start: 0.8204 (mmt) cc_final: 0.7948 (mmp) REVERT: B 43 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8416 (t0) REVERT: B 60 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7320 (ttp-170) REVERT: B 253 LYS cc_start: 0.7792 (tptt) cc_final: 0.7331 (tttm) REVERT: B 337 LEU cc_start: 0.8067 (tp) cc_final: 0.7848 (tt) outliers start: 15 outliers final: 9 residues processed: 83 average time/residue: 0.2494 time to fit residues: 25.8497 Evaluate side-chains 83 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER 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 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 307 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8450 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 6334 Z= 0.247 Angle : 0.491 8.253 8582 Z= 0.254 Chirality : 0.040 0.134 920 Planarity : 0.003 0.034 1082 Dihedral : 5.478 49.398 862 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.57 % Allowed : 12.54 % 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: 2.48 (0.31), residues: 760 helix: 3.79 (0.28), residues: 320 sheet: 1.13 (0.36), residues: 174 loop : -0.83 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS A 72 PHE 0.014 0.001 PHE B 371 TYR 0.007 0.001 TYR A 105 ARG 0.002 0.000 ARG B 397 *********************** 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 81 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.748 Fit side-chains REVERT: A 52 SER cc_start: 0.8898 (t) cc_final: 0.8677 (m) REVERT: A 145 LYS cc_start: 0.7789 (ttpp) cc_final: 0.7321 (tptp) REVERT: B 60 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7370 (ttp-170) outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.2334 time to fit residues: 22.9956 Evaluate side-chains 75 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8395 moved from start: 0.3929 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= 0.136 Angle : 0.440 9.088 8582 Z= 0.223 Chirality : 0.038 0.134 920 Planarity : 0.003 0.029 1082 Dihedral : 5.112 57.018 862 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.10 % Allowed : 13.79 % Favored : 85.11 % 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: 2.74 (0.32), residues: 760 helix: 4.09 (0.28), residues: 320 sheet: 1.13 (0.36), residues: 174 loop : -0.71 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS B 375 PHE 0.013 0.001 PHE B 371 TYR 0.005 0.001 TYR B 239 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 83 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.735 Fit side-chains REVERT: A 145 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7331 (tptp) REVERT: A 303 MET cc_start: 0.7012 (mmt) cc_final: 0.6802 (mmt) REVERT: B 60 ARG cc_start: 0.7574 (ttp80) cc_final: 0.7357 (ttp-170) REVERT: B 253 LYS cc_start: 0.7859 (tptt) cc_final: 0.7392 (tttm) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.2292 time to fit residues: 23.9958 Evaluate side-chains 74 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4044 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= 0.147 Angle : 0.440 8.334 8582 Z= 0.224 Chirality : 0.038 0.133 920 Planarity : 0.003 0.031 1082 Dihedral : 5.028 59.445 862 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.57 % Allowed : 13.32 % Favored : 85.11 % 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 (0.32), residues: 760 helix: 4.08 (0.28), residues: 320 sheet: 1.17 (0.36), residues: 174 loop : -0.70 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 310 HIS 0.004 0.001 HIS A 375 PHE 0.014 0.001 PHE B 371 TYR 0.005 0.001 TYR A 105 ARG 0.002 0.000 ARG A 32 *********************** 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 83 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.723 Fit side-chains REVERT: A 43 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8314 (t0) REVERT: A 145 LYS cc_start: 0.7834 (ttpp) cc_final: 0.7370 (tptp) REVERT: A 253 LYS cc_start: 0.7875 (tptt) cc_final: 0.7433 (tttm) REVERT: B 60 ARG cc_start: 0.7588 (ttp80) cc_final: 0.7336 (ttp-170) REVERT: B 253 LYS cc_start: 0.7863 (tptt) cc_final: 0.7387 (tttm) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.2279 time to fit residues: 23.7840 Evaluate side-chains 79 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 146 ASP 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: 6.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 6334 Z= 0.479 Angle : 0.606 9.293 8582 Z= 0.306 Chirality : 0.044 0.137 920 Planarity : 0.004 0.039 1082 Dihedral : 5.840 45.892 862 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.57 % Allowed : 13.32 % Favored : 85.11 % 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: 2.22 (0.31), residues: 760 helix: 3.40 (0.28), residues: 320 sheet: 1.20 (0.37), residues: 174 loop : -0.89 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 17 HIS 0.006 0.002 HIS B 72 PHE 0.018 0.002 PHE A 371 TYR 0.007 0.001 TYR A 105 ARG 0.003 0.000 ARG A 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 81 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.758 Fit side-chains REVERT: A 145 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7437 (tptp) REVERT: A 253 LYS cc_start: 0.7850 (tptt) cc_final: 0.7407 (tttm) REVERT: A 307 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7323 (ttmt) REVERT: B 60 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7352 (ttp-170) REVERT: B 253 LYS cc_start: 0.7835 (tptt) cc_final: 0.7354 (tttm) REVERT: B 303 MET cc_start: 0.7364 (ptp) cc_final: 0.7049 (mtt) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.2647 time to fit residues: 26.0660 Evaluate side-chains 76 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER 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 23 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.8450 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6334 Z= 0.206 Angle : 0.477 8.648 8582 Z= 0.242 Chirality : 0.039 0.134 920 Planarity : 0.003 0.038 1082 Dihedral : 5.330 49.574 862 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.57 % Allowed : 13.01 % Favored : 85.42 % 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 (0.32), residues: 760 helix: 3.73 (0.28), residues: 320 sheet: 1.17 (0.36), residues: 174 loop : -0.83 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS A 375 PHE 0.013 0.001 PHE A 371 TYR 0.005 0.001 TYR B 239 ARG 0.002 0.000 ARG A 8 *********************** 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 77 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.725 Fit side-chains REVERT: A 145 LYS cc_start: 0.7914 (ttpp) cc_final: 0.7412 (tptp) REVERT: A 307 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7222 (ttmt) REVERT: B 60 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7359 (ttp-170) REVERT: B 253 LYS cc_start: 0.7787 (tptt) cc_final: 0.7339 (tttm) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.2529 time to fit residues: 24.2190 Evaluate side-chains 74 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 66 THR 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 23 SER Chi-restraints excluded: chain B residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 0.0570 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6334 Z= 0.170 Angle : 0.460 8.636 8582 Z= 0.231 Chirality : 0.038 0.134 920 Planarity : 0.003 0.036 1082 Dihedral : 5.146 54.085 862 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.41 % Allowed : 13.17 % Favored : 85.42 % 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: 2.62 (0.32), residues: 760 helix: 3.92 (0.28), residues: 320 sheet: 1.17 (0.36), residues: 174 loop : -0.76 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.005 0.001 HIS A 375 PHE 0.011 0.001 PHE A 371 TYR 0.005 0.001 TYR B 239 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 77 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.770 Fit side-chains REVERT: A 145 LYS cc_start: 0.7966 (ttpp) cc_final: 0.7468 (tptp) REVERT: A 253 LYS cc_start: 0.7792 (tptt) cc_final: 0.7355 (tttm) REVERT: B 60 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7353 (ttp-170) REVERT: B 253 LYS cc_start: 0.7783 (tptt) cc_final: 0.7333 (tttm) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.2455 time to fit residues: 23.7527 Evaluate side-chains 72 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 0.0270 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.128477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.085929 restraints weight = 6899.164| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.10 r_work: 0.2625 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4207 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= 0.428 Angle : 0.585 8.675 8582 Z= 0.294 Chirality : 0.043 0.139 920 Planarity : 0.004 0.044 1082 Dihedral : 5.710 46.288 862 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.41 % Allowed : 13.32 % Favored : 85.27 % 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: 2.21 (0.31), residues: 760 helix: 3.44 (0.28), residues: 320 sheet: 1.16 (0.37), residues: 174 loop : -0.93 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 17 HIS 0.005 0.002 HIS B 72 PHE 0.011 0.002 PHE B 374 TYR 0.007 0.001 TYR A 105 ARG 0.003 0.000 ARG A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.89 seconds wall clock time: 29 minutes 47.21 seconds (1787.21 seconds total)