Starting phenix.real_space_refine on Thu Jul 18 19:10:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcx_18336/07_2024/8qcx_18336.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcx_18336/07_2024/8qcx_18336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcx_18336/07_2024/8qcx_18336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcx_18336/07_2024/8qcx_18336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcx_18336/07_2024/8qcx_18336.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcx_18336/07_2024/8qcx_18336.cif" } resolution = 3.1 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= 0.004 sd= 0.194 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 19 5.16 5 C 2182 2.51 5 N 521 2.21 5 O 561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3283 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3283 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406} Chain breaks: 1 Time building chain proxies: 2.50, per 1000 atoms: 0.76 Number of scatterers: 3283 At special positions: 0 Unit cell: (84.804, 56.154, 65.322, 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 19 16.00 O 561 8.00 N 521 7.00 C 2182 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: 1.36 Conformation dependent library (CDL) restraints added in 630.7 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 82 through 104 removed outlier: 4.291A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.113A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 169 removed outlier: 3.782A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) Proline residue: A 136 - end of helix removed outlier: 5.098A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 7.639A pdb=" N LEU A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N ARG A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 176 through 196 removed outlier: 3.585A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.650A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 232 removed outlier: 3.626A pdb=" N ILE A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 242 through 271 removed outlier: 3.807A pdb=" N TYR A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.614A pdb=" N ARG A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 330 Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.552A pdb=" N HIS A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 372 removed outlier: 3.704A pdb=" N VAL A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 396 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.831A pdb=" N VAL A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) Proline residue: A 420 - end of helix Processing helix chain 'A' and resid 434 through 465 Processing helix chain 'A' and resid 465 through 486 removed outlier: 3.703A pdb=" N GLY A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 272 hydrogen bonds defined for protein. 816 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: 0.92 Time building geometry restraints manager: 1.48 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: 984 1.34 - 1.46: 811 1.46 - 1.58: 1539 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3365 Sorted by residual: bond pdb=" N LYS A 273 " pdb=" CA LYS A 273 " ideal model delta sigma weight residual 1.452 1.495 -0.042 1.22e-02 6.72e+03 1.21e+01 bond pdb=" N VAL A 271 " pdb=" CA VAL A 271 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.67e+00 bond pdb=" N ASN A 307 " pdb=" CA ASN A 307 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.30e-02 5.92e+03 5.43e+00 bond pdb=" N SER A 127 " pdb=" CA SER A 127 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.32e-02 5.74e+03 5.29e+00 bond pdb=" N GLN A 284 " pdb=" CA GLN A 284 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.40e+00 ... (remaining 3360 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.32: 80 106.32 - 113.24: 1842 113.24 - 120.15: 1185 120.15 - 127.06: 1438 127.06 - 133.98: 37 Bond angle restraints: 4582 Sorted by residual: angle pdb=" CA LYS A 273 " pdb=" C LYS A 273 " pdb=" O LYS A 273 " ideal model delta sigma weight residual 121.88 117.31 4.57 1.30e+00 5.92e-01 1.24e+01 angle pdb=" N GLN A 284 " pdb=" CA GLN A 284 " pdb=" C GLN A 284 " ideal model delta sigma weight residual 111.36 107.61 3.75 1.09e+00 8.42e-01 1.18e+01 angle pdb=" CA PRO A 198 " pdb=" N PRO A 198 " pdb=" CD PRO A 198 " ideal model delta sigma weight residual 112.00 107.23 4.77 1.40e+00 5.10e-01 1.16e+01 angle pdb=" N SER A 127 " pdb=" CA SER A 127 " pdb=" C SER A 127 " ideal model delta sigma weight residual 113.50 109.40 4.10 1.23e+00 6.61e-01 1.11e+01 angle pdb=" CA LYS A 273 " pdb=" C LYS A 273 " pdb=" N GLU A 274 " ideal model delta sigma weight residual 115.63 119.70 -4.07 1.36e+00 5.41e-01 8.97e+00 ... (remaining 4577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 1726 16.06 - 32.12: 169 32.12 - 48.18: 35 48.18 - 64.24: 4 64.24 - 80.30: 3 Dihedral angle restraints: 1937 sinusoidal: 726 harmonic: 1211 Sorted by residual: dihedral pdb=" CA MET A 197 " pdb=" C MET A 197 " pdb=" N PRO A 198 " pdb=" CA PRO A 198 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TYR A 94 " pdb=" C TYR A 94 " pdb=" N SER A 95 " pdb=" CA SER A 95 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB GLU A 245 " pdb=" CG GLU A 245 " pdb=" CD GLU A 245 " pdb=" OE1 GLU A 245 " ideal model delta sinusoidal sigma weight residual 0.00 -80.30 80.30 1 3.00e+01 1.11e-03 8.87e+00 ... (remaining 1934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 430 0.046 - 0.092: 100 0.092 - 0.138: 11 0.138 - 0.184: 0 0.184 - 0.230: 2 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ASN A 307 " pdb=" N ASN A 307 " pdb=" C ASN A 307 " pdb=" CB ASN A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB VAL A 271 " pdb=" CA VAL A 271 " pdb=" CG1 VAL A 271 " pdb=" CG2 VAL A 271 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" CA PHE A 272 " pdb=" N PHE A 272 " pdb=" C PHE A 272 " pdb=" CB PHE A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.62 -0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 540 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 197 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO A 198 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 198 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 198 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 431 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 432 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 233 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 234 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.018 5.00e-02 4.00e+02 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 860 2.80 - 3.33: 3407 3.33 - 3.85: 5408 3.85 - 4.37: 6569 4.37 - 4.90: 11128 Nonbonded interactions: 27372 Sorted by model distance: nonbonded pdb=" O VAL A 391 " pdb=" OG1 THR A 395 " model vdw 2.275 2.440 nonbonded pdb=" OE1 GLU A 342 " pdb=" ND2 ASN A 345 " model vdw 2.310 2.520 nonbonded pdb=" NE1 TRP A 166 " pdb=" OG1 THR A 262 " model vdw 2.359 2.520 nonbonded pdb=" OG SER A 99 " pdb=" OD1 ASN A 222 " model vdw 2.361 2.440 nonbonded pdb=" OD2 ASP A 490 " pdb=" NH2 ARG A 492 " model vdw 2.386 2.520 ... (remaining 27367 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 0.042 3365 Z= 0.166 Angle : 0.505 6.060 4582 Z= 0.287 Chirality : 0.038 0.230 543 Planarity : 0.006 0.122 555 Dihedral : 13.428 80.295 1165 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.06 (0.41), residues: 418 helix: 0.99 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -0.54 (0.90), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 102 HIS 0.001 0.000 HIS A 175 PHE 0.007 0.001 PHE A 425 TYR 0.011 0.001 TYR A 94 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.324 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1201 time to fit residues: 7.7481 Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3365 Z= 0.189 Angle : 0.559 7.292 4582 Z= 0.302 Chirality : 0.039 0.143 543 Planarity : 0.005 0.081 555 Dihedral : 3.913 17.483 452 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.13 % Allowed : 7.08 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.41), residues: 418 helix: 1.86 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.71 (0.90), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 102 HIS 0.002 0.000 HIS A 338 PHE 0.013 0.001 PHE A 472 TYR 0.025 0.002 TYR A 94 ARG 0.004 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.356 Fit side-chains REVERT: A 197 MET cc_start: 0.8638 (ptt) cc_final: 0.8389 (ptt) REVERT: A 367 TRP cc_start: 0.8543 (t-100) cc_final: 0.8311 (t-100) REVERT: A 411 MET cc_start: 0.8074 (ttp) cc_final: 0.7851 (ttp) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.1100 time to fit residues: 7.6348 Evaluate side-chains 44 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 456 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7710 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3365 Z= 0.172 Angle : 0.533 7.041 4582 Z= 0.279 Chirality : 0.038 0.147 543 Planarity : 0.005 0.068 555 Dihedral : 3.935 17.920 452 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.70 % Allowed : 9.92 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.41), residues: 418 helix: 2.09 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.76 (0.90), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 102 HIS 0.002 0.001 HIS A 338 PHE 0.011 0.001 PHE A 220 TYR 0.026 0.001 TYR A 94 ARG 0.001 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.341 Fit side-chains REVERT: A 251 SER cc_start: 0.8580 (t) cc_final: 0.7960 (p) REVERT: A 384 MET cc_start: 0.8731 (mmm) cc_final: 0.8417 (mmm) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.1079 time to fit residues: 7.6747 Evaluate side-chains 51 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7691 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3365 Z= 0.150 Angle : 0.516 6.822 4582 Z= 0.269 Chirality : 0.037 0.148 543 Planarity : 0.005 0.062 555 Dihedral : 3.944 17.575 452 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.70 % Allowed : 11.33 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.42), residues: 418 helix: 2.17 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -0.51 (0.92), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 367 HIS 0.001 0.000 HIS A 338 PHE 0.011 0.001 PHE A 413 TYR 0.025 0.001 TYR A 94 ARG 0.002 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.362 Fit side-chains REVERT: A 251 SER cc_start: 0.8650 (t) cc_final: 0.8087 (p) REVERT: A 384 MET cc_start: 0.8687 (mmm) cc_final: 0.8394 (mmm) outliers start: 6 outliers final: 2 residues processed: 55 average time/residue: 0.1081 time to fit residues: 7.9807 Evaluate side-chains 50 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7728 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3365 Z= 0.213 Angle : 0.544 6.594 4582 Z= 0.283 Chirality : 0.038 0.159 543 Planarity : 0.005 0.057 555 Dihedral : 3.994 17.947 452 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.27 % Allowed : 13.03 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.42), residues: 418 helix: 2.22 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -0.51 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 85 HIS 0.002 0.001 HIS A 338 PHE 0.015 0.002 PHE A 413 TYR 0.026 0.001 TYR A 94 ARG 0.001 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.489 Fit side-chains REVERT: A 251 SER cc_start: 0.8593 (t) cc_final: 0.7966 (p) REVERT: A 272 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.6652 (t80) REVERT: A 384 MET cc_start: 0.8774 (mmm) cc_final: 0.8506 (mmm) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 0.1127 time to fit residues: 8.0602 Evaluate side-chains 53 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3365 Z= 0.242 Angle : 0.561 6.786 4582 Z= 0.292 Chirality : 0.039 0.163 543 Planarity : 0.005 0.054 555 Dihedral : 4.094 17.651 452 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.27 % Allowed : 14.73 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.42), residues: 418 helix: 2.16 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -0.64 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 337 HIS 0.002 0.001 HIS A 338 PHE 0.017 0.002 PHE A 413 TYR 0.026 0.002 TYR A 94 ARG 0.001 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.369 Fit side-chains REVERT: A 263 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8817 (tt) REVERT: A 272 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.6734 (t80) REVERT: A 389 MET cc_start: 0.7295 (tpt) cc_final: 0.7094 (tpt) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.0984 time to fit residues: 7.2334 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7749 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3365 Z= 0.230 Angle : 0.551 6.762 4582 Z= 0.287 Chirality : 0.038 0.159 543 Planarity : 0.005 0.054 555 Dihedral : 4.097 17.649 452 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.70 % Allowed : 15.30 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.41), residues: 418 helix: 2.17 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.74 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 337 HIS 0.002 0.001 HIS A 338 PHE 0.016 0.002 PHE A 413 TYR 0.025 0.001 TYR A 94 ARG 0.001 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.367 Fit side-chains REVERT: A 263 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8861 (tt) REVERT: A 272 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6847 (t80) REVERT: A 389 MET cc_start: 0.7312 (tpt) cc_final: 0.7070 (tpt) REVERT: A 495 LYS cc_start: 0.7410 (mttp) cc_final: 0.7140 (mtmt) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1130 time to fit residues: 7.5789 Evaluate side-chains 51 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3365 Z= 0.180 Angle : 0.521 6.563 4582 Z= 0.273 Chirality : 0.037 0.154 543 Planarity : 0.004 0.052 555 Dihedral : 4.047 17.360 452 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.70 % Allowed : 15.58 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.42), residues: 418 helix: 2.30 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.73 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 337 HIS 0.002 0.001 HIS A 338 PHE 0.015 0.001 PHE A 220 TYR 0.024 0.001 TYR A 94 ARG 0.001 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.399 Fit side-chains REVERT: A 263 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8822 (tt) REVERT: A 272 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.6780 (t80) REVERT: A 334 MET cc_start: 0.7754 (mtm) cc_final: 0.7435 (mtp) REVERT: A 384 MET cc_start: 0.8766 (mmm) cc_final: 0.8508 (mmm) REVERT: A 389 MET cc_start: 0.7311 (tpt) cc_final: 0.7051 (tpt) REVERT: A 495 LYS cc_start: 0.7409 (mttp) cc_final: 0.7152 (mtmt) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.1138 time to fit residues: 8.4462 Evaluate side-chains 53 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3365 Z= 0.213 Angle : 0.540 6.642 4582 Z= 0.281 Chirality : 0.038 0.159 543 Planarity : 0.005 0.051 555 Dihedral : 4.069 17.627 452 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.42 % Allowed : 15.58 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.42), residues: 418 helix: 2.28 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -0.76 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 337 HIS 0.002 0.001 HIS A 338 PHE 0.016 0.002 PHE A 413 TYR 0.025 0.001 TYR A 94 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.326 Fit side-chains REVERT: A 263 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8827 (tt) REVERT: A 272 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.6830 (t80) REVERT: A 384 MET cc_start: 0.8739 (mmm) cc_final: 0.8481 (mmm) REVERT: A 389 MET cc_start: 0.7395 (tpt) cc_final: 0.7085 (tpt) REVERT: A 495 LYS cc_start: 0.7423 (mttp) cc_final: 0.7164 (mtmt) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.1072 time to fit residues: 7.4347 Evaluate side-chains 52 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7716 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3365 Z= 0.167 Angle : 0.517 6.854 4582 Z= 0.269 Chirality : 0.037 0.153 543 Planarity : 0.004 0.051 555 Dihedral : 4.010 17.293 452 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.42 % Allowed : 15.86 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.41), residues: 418 helix: 2.38 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.76 (0.88), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 337 HIS 0.002 0.001 HIS A 338 PHE 0.015 0.001 PHE A 220 TYR 0.024 0.001 TYR A 94 ARG 0.001 0.000 ARG A 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.347 Fit side-chains REVERT: A 263 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8783 (tt) REVERT: A 272 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.6778 (t80) REVERT: A 298 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6235 (tp) REVERT: A 384 MET cc_start: 0.8772 (mmm) cc_final: 0.8520 (mmm) REVERT: A 389 MET cc_start: 0.7405 (tpt) cc_final: 0.7109 (tpt) REVERT: A 495 LYS cc_start: 0.7443 (mttp) cc_final: 0.7200 (mtmt) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.1112 time to fit residues: 8.3078 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.142921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113472 restraints weight = 4052.064| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.16 r_work: 0.2961 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3365 Z= 0.147 Angle : 0.507 6.635 4582 Z= 0.264 Chirality : 0.037 0.152 543 Planarity : 0.004 0.050 555 Dihedral : 3.966 17.249 452 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.42 % Allowed : 16.15 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.42), residues: 418 helix: 2.44 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.77 (0.91), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 337 HIS 0.001 0.000 HIS A 338 PHE 0.015 0.001 PHE A 220 TYR 0.025 0.001 TYR A 94 ARG 0.001 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1005.57 seconds wall clock time: 20 minutes 0.72 seconds (1200.72 seconds total)