Starting phenix.real_space_refine on Fri Aug 2 14:21:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybe_39117/08_2024/8ybe_39117.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybe_39117/08_2024/8ybe_39117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybe_39117/08_2024/8ybe_39117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybe_39117/08_2024/8ybe_39117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybe_39117/08_2024/8ybe_39117.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybe_39117/08_2024/8ybe_39117.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1873 2.51 5 N 473 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3110 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Conformer: "B" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} bond proxies already assigned to first conformer: 2936 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Classifications: {'water': 197} Link IDs: {None: 196} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 393 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 393 " occ=0.50 Time building chain proxies: 4.14, per 1000 atoms: 1.33 Number of scatterers: 3110 At special positions: 0 Unit cell: (50.0692, 62.7628, 77.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 758 8.00 N 473 7.00 C 1873 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 Links applied ALPHA1-4 " GLC B 1 " - " GLC B 2 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.0 seconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 684 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 54.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 68 through 80 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.716A pdb=" N GLY A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.768A pdb=" N THR A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.339A pdb=" N ASP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.795A pdb=" N GLU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 360 through 379 removed outlier: 4.457A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 64 removed outlier: 6.350A pdb=" N LEU A 33 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE A 35 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 85 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 34 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 87 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP A 36 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ALA A 89 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA A 290 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 8.222A pdb=" N SER A 171 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR A 251 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU A 173 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N ASN A 253 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA A 249 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 198 removed outlier: 3.668A pdb=" N LYS A 196 " --> pdb=" O ASP A 203 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 433 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: 0.91 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 544 1.32 - 1.44: 729 1.44 - 1.56: 1698 1.56 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 2983 Sorted by residual: bond pdb=" C ALA A 172 " pdb=" O ALA A 172 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.15e-02 7.56e+03 1.05e+01 bond pdb=" CA ARG A 380 " pdb=" C ARG A 380 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.29e-02 6.01e+03 9.19e+00 bond pdb=" CA LYS A 201 " pdb=" C LYS A 201 " ideal model delta sigma weight residual 1.519 1.486 0.034 1.14e-02 7.69e+03 8.68e+00 bond pdb=" C ALA A 327 " pdb=" O ALA A 327 " ideal model delta sigma weight residual 1.234 1.202 0.032 1.22e-02 6.72e+03 6.97e+00 bond pdb=" CA LYS A 32 " pdb=" C LYS A 32 " ideal model delta sigma weight residual 1.521 1.489 0.032 1.24e-02 6.50e+03 6.66e+00 ... (remaining 2978 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.44: 96 106.44 - 113.35: 1629 113.35 - 120.26: 1078 120.26 - 127.17: 1207 127.17 - 134.08: 40 Bond angle restraints: 4050 Sorted by residual: angle pdb=" N PRO A 357 " pdb=" CA PRO A 357 " pdb=" C PRO A 357 " ideal model delta sigma weight residual 111.68 102.68 9.00 1.67e+00 3.59e-01 2.90e+01 angle pdb=" N SER A 296 " pdb=" CA SER A 296 " pdb=" C SER A 296 " ideal model delta sigma weight residual 109.48 116.86 -7.38 1.44e+00 4.82e-01 2.63e+01 angle pdb=" N PRO A 297 " pdb=" CA PRO A 297 " pdb=" C PRO A 297 " ideal model delta sigma weight residual 114.35 108.38 5.97 1.25e+00 6.40e-01 2.28e+01 angle pdb=" C MET A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta sigma weight residual 120.14 115.17 4.97 1.06e+00 8.90e-01 2.20e+01 angle pdb=" O ASP A 91 " pdb=" C ASP A 91 " pdb=" N ARG A 92 " ideal model delta sigma weight residual 122.20 127.09 -4.89 1.14e+00 7.69e-01 1.84e+01 ... (remaining 4045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 1614 17.04 - 34.09: 132 34.09 - 51.13: 48 51.13 - 68.17: 16 68.17 - 85.21: 4 Dihedral angle restraints: 1814 sinusoidal: 744 harmonic: 1070 Sorted by residual: dihedral pdb=" CA ASP A 56 " pdb=" C ASP A 56 " pdb=" N THR A 57 " pdb=" CA THR A 57 " ideal model delta harmonic sigma weight residual 180.00 -164.28 -15.72 0 5.00e+00 4.00e-02 9.89e+00 dihedral pdb=" CB GLU A 137 " pdb=" CG GLU A 137 " pdb=" CD GLU A 137 " pdb=" OE1 GLU A 137 " ideal model delta sinusoidal sigma weight residual 0.00 85.21 -85.21 1 3.00e+01 1.11e-03 9.78e+00 dihedral pdb=" N GLN A 381 " pdb=" CA GLN A 381 " pdb=" CB GLN A 381 " pdb=" CG GLN A 381 " ideal model delta sinusoidal sigma weight residual -180.00 -121.35 -58.65 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 374 0.068 - 0.136: 65 0.136 - 0.204: 6 0.204 - 0.273: 0 0.273 - 0.341: 1 Chirality restraints: 446 Sorted by residual: chirality pdb=" C1 GLC B 2 " pdb=" O4 GLC B 1 " pdb=" C2 GLC B 2 " pdb=" O5 GLC B 2 " both_signs ideal model delta sigma weight residual False 2.40 2.44 -0.04 2.00e-02 2.50e+03 4.34e+00 chirality pdb=" C1 GLC B 1 " pdb=" C2 GLC B 1 " pdb=" O1 GLC B 1 " pdb=" O5 GLC B 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA MET A 347 " pdb=" N MET A 347 " pdb=" C MET A 347 " pdb=" CB MET A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 443 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 92 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" C ARG A 92 " 0.077 2.00e-02 2.50e+03 pdb=" O ARG A 92 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE A 93 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 392 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR A 392 " 0.049 2.00e-02 2.50e+03 pdb=" O THR A 392 " -0.018 2.00e-02 2.50e+03 pdb=" N AARG A 393 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 392 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C THR A 392 " 0.048 2.00e-02 2.50e+03 pdb=" O THR A 392 " -0.018 2.00e-02 2.50e+03 pdb=" N BARG A 393 " -0.016 2.00e-02 2.50e+03 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 772 2.77 - 3.30: 3381 3.30 - 3.83: 6978 3.83 - 4.37: 8256 4.37 - 4.90: 12524 Nonbonded interactions: 31911 Sorted by model distance: nonbonded pdb=" OH TYR A 193 " pdb=" OD1 ASP A 206 " model vdw 2.236 3.040 nonbonded pdb=" O VAL A 76 " pdb=" OG1 THR A 79 " model vdw 2.298 3.040 nonbonded pdb=" O HOH A 454 " pdb=" O HOH A 592 " model vdw 2.327 3.040 nonbonded pdb=" OD2 ASP A 262 " pdb=" O HOH A 401 " model vdw 2.330 3.040 nonbonded pdb=" O THR A 248 " pdb=" O HOH A 402 " model vdw 2.330 3.040 ... (remaining 31906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.410 Find NCS groups from input model: 0.030 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:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 2983 Z= 0.400 Angle : 0.888 9.000 4050 Z= 0.529 Chirality : 0.053 0.341 446 Planarity : 0.008 0.061 521 Dihedral : 15.835 85.214 1130 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.34 % Allowed : 13.38 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.41), residues: 371 helix: 0.91 (0.33), residues: 192 sheet: 0.98 (0.79), residues: 29 loop : 1.15 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 88 HIS 0.004 0.001 HIS A 229 PHE 0.013 0.002 PHE A 220 TYR 0.022 0.002 TYR A 181 ARG 0.003 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.353 Fit side-chains REVERT: A 29 GLU cc_start: 0.6751 (tt0) cc_final: 0.5984 (mm-30) REVERT: A 98 GLN cc_start: 0.7692 (tp40) cc_final: 0.7436 (tm-30) REVERT: A 128 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7932 (mtpm) REVERT: A 197 TYR cc_start: 0.7370 (t80) cc_final: 0.6600 (t80) REVERT: A 284 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.6140 (m-10) REVERT: A 354 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6670 (pm20) outliers start: 6 outliers final: 1 residues processed: 55 average time/residue: 1.3765 time to fit residues: 77.7051 Evaluate side-chains 37 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2983 Z= 0.249 Angle : 0.640 7.031 4050 Z= 0.340 Chirality : 0.044 0.153 446 Planarity : 0.005 0.054 521 Dihedral : 6.920 64.579 439 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.34 % Allowed : 15.72 % Favored : 81.94 % 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: 1.46 (0.42), residues: 371 helix: 0.89 (0.34), residues: 192 sheet: 0.66 (0.98), residues: 24 loop : 1.43 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 184 HIS 0.002 0.001 HIS A 90 PHE 0.012 0.002 PHE A 220 TYR 0.024 0.002 TYR A 181 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.324 Fit side-chains REVERT: A 98 GLN cc_start: 0.7660 (tp40) cc_final: 0.7436 (tm-30) REVERT: A 128 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7697 (mtpm) REVERT: A 179 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8036 (mm-30) outliers start: 6 outliers final: 1 residues processed: 46 average time/residue: 1.2651 time to fit residues: 59.9568 Evaluate side-chains 38 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 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 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2983 Z= 0.263 Angle : 0.623 7.161 4050 Z= 0.328 Chirality : 0.043 0.120 446 Planarity : 0.005 0.051 521 Dihedral : 5.294 52.396 436 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.00 % Allowed : 16.39 % Favored : 82.61 % 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: 1.43 (0.43), residues: 371 helix: 0.83 (0.35), residues: 192 sheet: 0.17 (0.98), residues: 24 loop : 1.57 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 PHE 0.013 0.002 PHE A 243 TYR 0.019 0.002 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.346 Fit side-chains REVERT: A 98 GLN cc_start: 0.7668 (tp40) cc_final: 0.7442 (tm-30) REVERT: A 317 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: A 321 LYS cc_start: 0.7796 (mptp) cc_final: 0.7246 (tttm) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 1.2885 time to fit residues: 58.4499 Evaluate side-chains 38 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 317 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2983 Z= 0.253 Angle : 0.612 6.841 4050 Z= 0.319 Chirality : 0.043 0.121 446 Planarity : 0.005 0.049 521 Dihedral : 5.254 52.862 436 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.34 % Allowed : 16.72 % Favored : 81.94 % 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: 1.40 (0.44), residues: 371 helix: 0.81 (0.35), residues: 192 sheet: -0.13 (0.99), residues: 24 loop : 1.59 (0.57), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 PHE 0.013 0.002 PHE A 243 TYR 0.017 0.001 TYR A 181 ARG 0.001 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.376 Fit side-chains REVERT: A 98 GLN cc_start: 0.7683 (tp40) cc_final: 0.7451 (tm-30) REVERT: A 179 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 317 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: A 321 LYS cc_start: 0.7775 (mptp) cc_final: 0.7237 (tttm) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 1.4004 time to fit residues: 61.9677 Evaluate side-chains 38 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 317 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2983 Z= 0.210 Angle : 0.568 6.787 4050 Z= 0.296 Chirality : 0.042 0.120 446 Planarity : 0.004 0.047 521 Dihedral : 5.095 53.075 436 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.67 % Allowed : 15.72 % Favored : 82.61 % 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: 1.44 (0.45), residues: 371 helix: 0.89 (0.35), residues: 192 sheet: -0.28 (0.99), residues: 24 loop : 1.58 (0.58), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 184 HIS 0.003 0.002 HIS A 90 PHE 0.011 0.002 PHE A 243 TYR 0.017 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.341 Fit side-chains REVERT: A 27 LYS cc_start: 0.5461 (OUTLIER) cc_final: 0.4878 (mtmt) REVERT: A 32 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7940 (mtpm) REVERT: A 92 ARG cc_start: 0.7758 (mmt180) cc_final: 0.7463 (mmm160) REVERT: A 179 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8065 (mm-30) REVERT: A 304 GLU cc_start: 0.8148 (tp30) cc_final: 0.7855 (tp30) REVERT: A 317 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: A 321 LYS cc_start: 0.7748 (mptp) cc_final: 0.7285 (tttm) outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 1.4622 time to fit residues: 64.5332 Evaluate side-chains 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 317 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2983 Z= 0.260 Angle : 0.617 7.001 4050 Z= 0.318 Chirality : 0.043 0.119 446 Planarity : 0.005 0.048 521 Dihedral : 5.195 53.011 436 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.34 % Allowed : 15.05 % Favored : 82.61 % 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: 1.43 (0.45), residues: 371 helix: 0.90 (0.35), residues: 192 sheet: -0.42 (1.01), residues: 24 loop : 1.57 (0.58), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 184 HIS 0.005 0.002 HIS A 90 PHE 0.013 0.002 PHE A 243 TYR 0.015 0.002 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.346 Fit side-chains REVERT: A 27 LYS cc_start: 0.5505 (OUTLIER) cc_final: 0.4911 (mtmt) REVERT: A 92 ARG cc_start: 0.7835 (mmt180) cc_final: 0.7525 (mmm160) REVERT: A 237 SER cc_start: 0.8212 (m) cc_final: 0.8010 (t) REVERT: A 317 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: A 321 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7280 (tttm) outliers start: 6 outliers final: 1 residues processed: 40 average time/residue: 1.4190 time to fit residues: 58.4068 Evaluate side-chains 39 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2983 Z= 0.241 Angle : 0.606 6.898 4050 Z= 0.313 Chirality : 0.042 0.119 446 Planarity : 0.004 0.047 521 Dihedral : 5.176 53.344 436 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.67 % Allowed : 16.72 % Favored : 81.61 % 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: 1.41 (0.45), residues: 371 helix: 0.89 (0.36), residues: 192 sheet: -0.56 (1.00), residues: 24 loop : 1.57 (0.58), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 PHE 0.013 0.002 PHE A 243 TYR 0.016 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.323 Fit side-chains REVERT: A 92 ARG cc_start: 0.7833 (mmt180) cc_final: 0.7528 (mmm160) REVERT: A 179 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 304 GLU cc_start: 0.8171 (tp30) cc_final: 0.7886 (tp30) REVERT: A 317 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: A 321 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7290 (tttm) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 1.4369 time to fit residues: 60.5279 Evaluate side-chains 38 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2983 Z= 0.284 Angle : 0.638 7.097 4050 Z= 0.330 Chirality : 0.043 0.121 446 Planarity : 0.005 0.048 521 Dihedral : 5.281 52.910 436 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.67 % Allowed : 17.39 % Favored : 80.94 % 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: 1.36 (0.45), residues: 371 helix: 0.83 (0.35), residues: 192 sheet: -0.60 (1.01), residues: 24 loop : 1.60 (0.58), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 184 HIS 0.006 0.002 HIS A 90 PHE 0.014 0.003 PHE A 243 TYR 0.014 0.002 TYR A 181 ARG 0.001 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.348 Fit side-chains REVERT: A 284 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.5915 (m-10) REVERT: A 304 GLU cc_start: 0.8186 (tp30) cc_final: 0.7903 (tp30) REVERT: A 317 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: A 321 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7278 (tttm) outliers start: 4 outliers final: 0 residues processed: 38 average time/residue: 1.3329 time to fit residues: 52.2035 Evaluate side-chains 37 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2983 Z= 0.204 Angle : 0.583 6.431 4050 Z= 0.299 Chirality : 0.041 0.120 446 Planarity : 0.004 0.045 521 Dihedral : 5.084 53.740 436 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.00 % Allowed : 18.06 % Favored : 80.94 % 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: 1.33 (0.45), residues: 371 helix: 0.85 (0.36), residues: 195 sheet: -0.65 (1.00), residues: 24 loop : 1.53 (0.58), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 184 HIS 0.003 0.002 HIS A 90 PHE 0.011 0.002 PHE A 243 TYR 0.017 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.466 Fit side-chains REVERT: A 92 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7493 (mmm160) REVERT: A 179 GLU cc_start: 0.8227 (mm-30) cc_final: 0.8013 (mm-30) REVERT: A 235 ASP cc_start: 0.8595 (p0) cc_final: 0.8335 (p0) REVERT: A 314 GLU cc_start: 0.6944 (mp0) cc_final: 0.6672 (mp0) REVERT: A 317 GLU cc_start: 0.7706 (tt0) cc_final: 0.7479 (tt0) REVERT: A 321 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7281 (tttm) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 1.4953 time to fit residues: 63.2399 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.0270 chunk 30 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2983 Z= 0.229 Angle : 0.607 7.366 4050 Z= 0.311 Chirality : 0.042 0.119 446 Planarity : 0.004 0.046 521 Dihedral : 5.122 53.265 436 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.34 % Allowed : 17.39 % Favored : 81.27 % 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: 1.30 (0.45), residues: 371 helix: 0.81 (0.36), residues: 195 sheet: -0.67 (1.00), residues: 24 loop : 1.53 (0.58), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 88 HIS 0.004 0.002 HIS A 90 PHE 0.012 0.002 PHE A 243 TYR 0.015 0.001 TYR A 181 ARG 0.002 0.000 ARG A 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.346 Fit side-chains REVERT: A 92 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7510 (mmm160) REVERT: A 304 GLU cc_start: 0.8183 (tp30) cc_final: 0.7953 (tp30) REVERT: A 314 GLU cc_start: 0.6958 (mp0) cc_final: 0.6690 (mp0) REVERT: A 317 GLU cc_start: 0.7704 (tt0) cc_final: 0.7474 (tt0) REVERT: A 321 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7256 (tttm) outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 1.4114 time to fit residues: 56.6615 Evaluate side-chains 38 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.145543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128788 restraints weight = 10956.140| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.92 r_work: 0.3280 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2983 Z= 0.251 Angle : 0.630 7.353 4050 Z= 0.323 Chirality : 0.042 0.119 446 Planarity : 0.004 0.046 521 Dihedral : 5.201 53.444 436 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.34 % Allowed : 17.73 % Favored : 80.94 % 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: 1.25 (0.45), residues: 371 helix: 0.76 (0.36), residues: 195 sheet: -0.78 (1.00), residues: 24 loop : 1.53 (0.58), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 184 HIS 0.005 0.002 HIS A 90 PHE 0.013 0.002 PHE A 243 TYR 0.015 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1728.37 seconds wall clock time: 31 minutes 12.19 seconds (1872.19 seconds total)