Starting phenix.real_space_refine on Fri Apr 5 20:17:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/04_2024/8i6j_35199_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/04_2024/8i6j_35199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/04_2024/8i6j_35199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/04_2024/8i6j_35199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/04_2024/8i6j_35199_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/04_2024/8i6j_35199_updated.pdb" } resolution = 3.82 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= 0.003 sd= 0.072 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 P 2 5.49 5 S 36 5.16 5 C 3318 2.51 5 N 925 2.21 5 O 1006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 105": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5287 Number of models: 1 Model: "" Number of chains: 3 Chain: "Q" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3889 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 16, 'TRANS': 483} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.88, per 1000 atoms: 0.73 Number of scatterers: 5287 At special positions: 0 Unit cell: (97.18, 74.58, 118.65, 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 36 16.00 P 2 15.00 O 1006 8.00 N 925 7.00 C 3318 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: 3.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 6 sheets defined 44.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'Q' and resid 66 through 83 removed outlier: 4.704A pdb=" N LYS Q 83 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 140 removed outlier: 3.644A pdb=" N HIS Q 133 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 184 No H-bonds generated for 'chain 'Q' and resid 181 through 184' Processing helix chain 'Q' and resid 191 through 201 removed outlier: 4.795A pdb=" N SER Q 201 " --> pdb=" O LYS Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 219 through 230 Processing helix chain 'C' and resid 21 through 36 removed outlier: 4.281A pdb=" N ASN C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 75 through 88 removed outlier: 4.008A pdb=" N SER C 84 " --> pdb=" O MET C 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 119 through 139 removed outlier: 3.542A pdb=" N LYS C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 261 through 283 removed outlier: 3.766A pdb=" N GLU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 274 " --> pdb=" O MET C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 317 through 323 Processing helix chain 'C' and resid 382 through 403 removed outlier: 3.761A pdb=" N LEU C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 429 Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 446 through 455 Processing helix chain 'C' and resid 459 through 472 Processing helix chain 'C' and resid 500 through 518 Processing sheet with id= A, first strand: chain 'Q' and resid 117 through 119 removed outlier: 3.735A pdb=" N PHE Q 167 " --> pdb=" O LEU Q 117 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 48 through 51 Processing sheet with id= C, first strand: chain 'C' and resid 201 through 205 removed outlier: 6.572A pdb=" N ILE C 374 " --> pdb=" O GLU C 202 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE C 204 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C 376 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 373 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 375 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 218 through 220 removed outlier: 3.504A pdb=" N ILE C 363 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 238 through 240 removed outlier: 6.169A pdb=" N VAL C 289 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR C 310 " --> pdb=" O VAL C 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 407 through 409 211 hydrogen bonds defined for protein. 612 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: 1.42 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1769 1.34 - 1.46: 950 1.46 - 1.58: 2578 1.58 - 1.70: 3 1.70 - 1.81: 60 Bond restraints: 5360 Sorted by residual: bond pdb=" CG GLU C 511 " pdb=" CD GLU C 511 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CG GLU Q 195 " pdb=" CD GLU Q 195 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 8.77e-01 bond pdb=" CG ARG Q 225 " pdb=" CD ARG Q 225 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.66e-01 bond pdb=" N GLN Q 122 " pdb=" CA GLN Q 122 " ideal model delta sigma weight residual 1.456 1.466 -0.010 1.23e-02 6.61e+03 6.28e-01 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.28: 136 106.28 - 113.72: 3101 113.72 - 121.15: 2596 121.15 - 128.59: 1373 128.59 - 136.03: 31 Bond angle restraints: 7237 Sorted by residual: angle pdb=" N ILE C 195 " pdb=" CA ILE C 195 " pdb=" C ILE C 195 " ideal model delta sigma weight residual 113.53 109.98 3.55 9.80e-01 1.04e+00 1.31e+01 angle pdb=" N GLU C 511 " pdb=" CA GLU C 511 " pdb=" CB GLU C 511 " ideal model delta sigma weight residual 110.28 115.50 -5.22 1.55e+00 4.16e-01 1.13e+01 angle pdb=" N MET Q 73 " pdb=" CA MET Q 73 " pdb=" CB MET Q 73 " ideal model delta sigma weight residual 110.28 115.16 -4.88 1.55e+00 4.16e-01 9.91e+00 angle pdb=" N GLU Q 195 " pdb=" CA GLU Q 195 " pdb=" CB GLU Q 195 " ideal model delta sigma weight residual 110.12 114.56 -4.44 1.47e+00 4.63e-01 9.13e+00 angle pdb=" N TYR Q 102 " pdb=" CA TYR Q 102 " pdb=" C TYR Q 102 " ideal model delta sigma weight residual 110.80 116.86 -6.06 2.13e+00 2.20e-01 8.11e+00 ... (remaining 7232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.12: 3189 27.12 - 54.23: 131 54.23 - 81.35: 9 81.35 - 108.46: 5 108.46 - 135.58: 1 Dihedral angle restraints: 3335 sinusoidal: 1393 harmonic: 1942 Sorted by residual: dihedral pdb=" O2A ADP C 601 " pdb=" O3A ADP C 601 " pdb=" PA ADP C 601 " pdb=" PB ADP C 601 " ideal model delta sinusoidal sigma weight residual 300.00 164.42 135.58 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" CA ILE Q 150 " pdb=" C ILE Q 150 " pdb=" N SER Q 151 " pdb=" CA SER Q 151 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR Q 169 " pdb=" C TYR Q 169 " pdb=" N LEU Q 170 " pdb=" CA LEU Q 170 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 514 0.032 - 0.065: 209 0.065 - 0.097: 69 0.097 - 0.129: 47 0.129 - 0.162: 7 Chirality restraints: 846 Sorted by residual: chirality pdb=" CB ILE C 374 " pdb=" CA ILE C 374 " pdb=" CG1 ILE C 374 " pdb=" CG2 ILE C 374 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA GLU C 511 " pdb=" N GLU C 511 " pdb=" C GLU C 511 " pdb=" CB GLU C 511 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA TYR Q 102 " pdb=" N TYR Q 102 " pdb=" C TYR Q 102 " pdb=" CB TYR Q 102 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 843 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 112 " 0.014 2.00e-02 2.50e+03 1.41e-02 3.47e+00 pdb=" CG PHE C 112 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 112 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 112 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 112 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 112 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 124 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO Q 125 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO Q 125 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO Q 125 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 507 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C LYS C 507 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS C 507 " 0.009 2.00e-02 2.50e+03 pdb=" N THR C 508 " 0.008 2.00e-02 2.50e+03 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1165 2.79 - 3.32: 5171 3.32 - 3.85: 7880 3.85 - 4.37: 8299 4.37 - 4.90: 14516 Nonbonded interactions: 37031 Sorted by model distance: nonbonded pdb=" OD2 ASP C 132 " pdb=" OH TYR C 437 " model vdw 2.265 2.440 nonbonded pdb=" O VAL Q 183 " pdb=" NZ LYS Q 197 " model vdw 2.292 2.520 nonbonded pdb=" OE1 GLU C 497 " pdb=" NZ LYS C 502 " model vdw 2.341 2.520 nonbonded pdb=" O ASN Q 157 " pdb=" ND2 ASN Q 157 " model vdw 2.344 2.520 nonbonded pdb=" O SER C 158 " pdb=" OG1 THR C 161 " model vdw 2.348 2.440 ... (remaining 37026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.190 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 23.200 Find NCS groups from input model: 0.160 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 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 : 0.003 0.029 5360 Z= 0.196 Angle : 0.697 8.081 7237 Z= 0.359 Chirality : 0.046 0.162 846 Planarity : 0.004 0.040 921 Dihedral : 14.716 135.578 2075 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.17 % Allowed : 0.00 % Favored : 99.83 % 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: -0.94 (0.33), residues: 666 helix: 1.57 (0.31), residues: 306 sheet: -0.75 (0.66), residues: 70 loop : -3.23 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 435 HIS 0.004 0.001 HIS C 111 PHE 0.032 0.002 PHE C 112 TYR 0.011 0.002 TYR Q 102 ARG 0.009 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7745 (mmt) cc_final: 0.7351 (mmm) REVERT: C 190 ARG cc_start: 0.7336 (mmp80) cc_final: 0.7102 (mmp80) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2017 time to fit residues: 21.6836 Evaluate side-chains 75 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.0942 ------------------------------------------------------------------------------- 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: 0.7015 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5360 Z= 0.257 Angle : 0.669 8.347 7237 Z= 0.333 Chirality : 0.045 0.144 846 Planarity : 0.004 0.041 921 Dihedral : 7.242 135.187 736 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 1.03 % Allowed : 11.51 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.33), residues: 666 helix: 1.63 (0.31), residues: 305 sheet: -0.83 (0.62), residues: 78 loop : -3.33 (0.30), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 435 HIS 0.004 0.001 HIS C 74 PHE 0.014 0.002 PHE Q 167 TYR 0.014 0.002 TYR C 247 ARG 0.004 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.613 Fit side-chains REVERT: C 275 ILE cc_start: 0.9016 (mm) cc_final: 0.8779 (mm) REVERT: C 511 GLU cc_start: 0.7928 (mp0) cc_final: 0.7579 (mp0) outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 0.1977 time to fit residues: 20.9770 Evaluate side-chains 78 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5360 Z= 0.185 Angle : 0.609 7.082 7237 Z= 0.300 Chirality : 0.043 0.142 846 Planarity : 0.003 0.039 921 Dihedral : 7.110 136.139 736 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.23 % Allowed : 14.60 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.33), residues: 666 helix: 1.81 (0.31), residues: 303 sheet: -0.77 (0.62), residues: 78 loop : -3.33 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 435 HIS 0.002 0.001 HIS C 226 PHE 0.011 0.001 PHE C 362 TYR 0.011 0.001 TYR C 247 ARG 0.003 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: C 190 ARG cc_start: 0.7351 (mmp80) cc_final: 0.7129 (mmp80) REVERT: C 275 ILE cc_start: 0.8890 (mm) cc_final: 0.8565 (mm) REVERT: C 376 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8070 (pt) outliers start: 13 outliers final: 6 residues processed: 87 average time/residue: 0.1799 time to fit residues: 20.2372 Evaluate side-chains 79 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 10.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5360 Z= 0.215 Angle : 0.647 8.463 7237 Z= 0.319 Chirality : 0.044 0.149 846 Planarity : 0.003 0.038 921 Dihedral : 7.144 135.941 736 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.92 % Allowed : 15.64 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.33), residues: 666 helix: 1.81 (0.31), residues: 304 sheet: -0.80 (0.61), residues: 78 loop : -3.32 (0.30), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 435 HIS 0.003 0.001 HIS C 226 PHE 0.018 0.002 PHE Q 167 TYR 0.015 0.002 TYR C 247 ARG 0.005 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8148 (pptt) cc_final: 0.7739 (pptt) REVERT: C 376 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7764 (pt) REVERT: C 402 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.5202 (mt) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.1749 time to fit residues: 20.2027 Evaluate side-chains 89 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5360 Z= 0.225 Angle : 0.646 7.372 7237 Z= 0.321 Chirality : 0.044 0.153 846 Planarity : 0.003 0.038 921 Dihedral : 7.162 136.200 736 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.26 % Allowed : 17.70 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.33), residues: 666 helix: 1.58 (0.31), residues: 313 sheet: -0.81 (0.62), residues: 78 loop : -3.30 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 196 HIS 0.004 0.001 HIS C 74 PHE 0.018 0.002 PHE Q 167 TYR 0.015 0.002 TYR C 274 ARG 0.006 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 ARG cc_start: 0.7312 (mmp80) cc_final: 0.7069 (mmp80) REVERT: C 376 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7844 (pt) outliers start: 19 outliers final: 15 residues processed: 87 average time/residue: 0.1760 time to fit residues: 20.0114 Evaluate side-chains 90 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 47 optimal weight: 0.0010 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5360 Z= 0.152 Angle : 0.610 8.503 7237 Z= 0.297 Chirality : 0.042 0.140 846 Planarity : 0.003 0.036 921 Dihedral : 6.971 135.939 736 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.09 % Allowed : 19.24 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.33), residues: 666 helix: 1.82 (0.31), residues: 306 sheet: -0.62 (0.62), residues: 78 loop : -3.28 (0.30), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 196 HIS 0.002 0.001 HIS C 226 PHE 0.011 0.001 PHE C 264 TYR 0.019 0.001 TYR C 274 ARG 0.003 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7682 (mmt) cc_final: 0.7397 (mmm) REVERT: C 128 LYS cc_start: 0.8122 (pptt) cc_final: 0.7839 (pptt) REVERT: C 402 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.5901 (tt) outliers start: 18 outliers final: 13 residues processed: 91 average time/residue: 0.1798 time to fit residues: 21.5154 Evaluate side-chains 90 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5360 Z= 0.241 Angle : 0.660 9.160 7237 Z= 0.328 Chirality : 0.045 0.171 846 Planarity : 0.003 0.038 921 Dihedral : 7.087 135.353 736 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 3.09 % Allowed : 20.45 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.33), residues: 666 helix: 1.72 (0.31), residues: 306 sheet: -0.74 (0.63), residues: 78 loop : -3.33 (0.30), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 435 HIS 0.004 0.001 HIS C 74 PHE 0.018 0.002 PHE Q 167 TYR 0.022 0.002 TYR C 437 ARG 0.007 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 376 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7848 (pt) outliers start: 18 outliers final: 13 residues processed: 91 average time/residue: 0.1688 time to fit residues: 20.1915 Evaluate side-chains 92 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.0870 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 0.0770 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.0670 chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 47 optimal weight: 0.0970 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5360 Z= 0.144 Angle : 0.606 7.509 7237 Z= 0.299 Chirality : 0.042 0.135 846 Planarity : 0.003 0.034 921 Dihedral : 6.873 134.349 736 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.58 % Allowed : 21.31 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.33), residues: 666 helix: 1.83 (0.31), residues: 303 sheet: -0.46 (0.63), residues: 78 loop : -3.24 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.002 0.001 HIS C 226 PHE 0.012 0.001 PHE C 264 TYR 0.012 0.001 TYR C 274 ARG 0.005 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 102 TYR cc_start: 0.6259 (OUTLIER) cc_final: 0.5973 (p90) REVERT: Q 187 MET cc_start: 0.7607 (mmt) cc_final: 0.7392 (mmm) REVERT: C 128 LYS cc_start: 0.7829 (pptt) cc_final: 0.7455 (pptt) REVERT: C 190 ARG cc_start: 0.7216 (mmp80) cc_final: 0.6928 (mmp80) REVERT: C 376 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8091 (pt) REVERT: C 402 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.5898 (tt) outliers start: 15 outliers final: 11 residues processed: 92 average time/residue: 0.1924 time to fit residues: 22.8646 Evaluate side-chains 92 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 102 TYR Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 169 TYR Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5360 Z= 0.174 Angle : 0.641 9.351 7237 Z= 0.315 Chirality : 0.043 0.146 846 Planarity : 0.003 0.035 921 Dihedral : 6.837 132.987 736 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.09 % Allowed : 20.96 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.33), residues: 666 helix: 1.84 (0.31), residues: 306 sheet: -0.59 (0.69), residues: 63 loop : -2.93 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.004 0.001 HIS C 226 PHE 0.013 0.001 PHE C 264 TYR 0.011 0.001 TYR C 274 ARG 0.006 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7701 (mmt) cc_final: 0.7455 (mmm) REVERT: C 128 LYS cc_start: 0.8157 (pptt) cc_final: 0.7789 (pptt) REVERT: C 376 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8152 (pt) REVERT: C 402 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.5663 (mt) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.1752 time to fit residues: 21.1026 Evaluate side-chains 92 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 169 TYR Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 0.0670 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 22 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5360 Z= 0.177 Angle : 0.665 10.892 7237 Z= 0.325 Chirality : 0.044 0.192 846 Planarity : 0.003 0.034 921 Dihedral : 6.836 131.694 736 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.92 % Allowed : 21.82 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.33), residues: 666 helix: 1.83 (0.31), residues: 306 sheet: -0.28 (0.63), residues: 78 loop : -3.15 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.003 0.001 HIS C 226 PHE 0.014 0.001 PHE C 264 TYR 0.010 0.001 TYR C 274 ARG 0.006 0.000 ARG Q 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7644 (mmt) cc_final: 0.7429 (mmm) REVERT: C 128 LYS cc_start: 0.8186 (pptt) cc_final: 0.7806 (pptt) REVERT: C 190 ARG cc_start: 0.7230 (mmp80) cc_final: 0.6908 (mmp80) REVERT: C 376 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8151 (pt) REVERT: C 402 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.5676 (mt) outliers start: 17 outliers final: 14 residues processed: 90 average time/residue: 0.1792 time to fit residues: 21.0042 Evaluate side-chains 93 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 169 TYR Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.210999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.173524 restraints weight = 8206.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.176482 restraints weight = 12752.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.176806 restraints weight = 9454.461| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5360 Z= 0.195 Angle : 0.672 10.152 7237 Z= 0.330 Chirality : 0.044 0.185 846 Planarity : 0.003 0.036 921 Dihedral : 6.829 131.013 736 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 2.92 % Allowed : 21.82 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.34), residues: 666 helix: 1.74 (0.31), residues: 306 sheet: -0.35 (0.63), residues: 78 loop : -3.18 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.003 0.001 HIS C 226 PHE 0.014 0.002 PHE C 264 TYR 0.010 0.001 TYR C 274 ARG 0.006 0.000 ARG Q 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1439.90 seconds wall clock time: 27 minutes 13.62 seconds (1633.62 seconds total)