Starting phenix.real_space_refine on Fri Dec 27 11:30:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7w_33672/12_2024/7y7w_33672.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7w_33672/12_2024/7y7w_33672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7w_33672/12_2024/7y7w_33672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7w_33672/12_2024/7y7w_33672.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7w_33672/12_2024/7y7w_33672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7w_33672/12_2024/7y7w_33672.cif" } resolution = 2.4 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= 0.002 sd= 0.098 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2844 2.51 5 N 655 2.21 5 O 774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 22, 'TRANS': 506} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 100 Unusual residues: {' CL': 1, ' NA': 2, 'ABU': 1, 'NAG': 3} Classifications: {'undetermined': 7, 'water': 48} Link IDs: {None: 54} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.15, per 1000 atoms: 0.73 Number of scatterers: 4310 At special positions: 0 Unit cell: (67.115, 72.5275, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 774 8.00 N 655 7.00 C 2844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 548.9 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 966 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 82.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.734A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.743A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.990A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 4.051A pdb=" N GLN A 163 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.579A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.941A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 Processing helix chain 'A' and resid 315 through 350 removed outlier: 3.709A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 362 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.766A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.174A pdb=" N THR A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 removed outlier: 4.096A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 474 removed outlier: 3.683A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.487A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 546 removed outlier: 3.637A pdb=" N GLN A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.550A pdb=" N MET A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 569 removed outlier: 4.460A pdb=" N VAL A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 283 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 620 1.29 - 1.42: 1312 1.42 - 1.55: 2407 1.55 - 1.68: 0 1.68 - 1.81: 54 Bond restraints: 4393 Sorted by residual: bond pdb=" C ASP A 395 " pdb=" O ASP A 395 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C PHE A 53 " pdb=" O PHE A 53 " ideal model delta sigma weight residual 1.237 1.183 0.053 1.19e-02 7.06e+03 2.01e+01 bond pdb=" C SER A 396 " pdb=" O SER A 396 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" CG ASP A 395 " pdb=" OD1 ASP A 395 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.75e+00 ... (remaining 4388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 5835 2.22 - 4.45: 128 4.45 - 6.67: 14 6.67 - 8.89: 4 8.89 - 11.12: 1 Bond angle restraints: 5982 Sorted by residual: angle pdb=" CA ASP A 395 " pdb=" CB ASP A 395 " pdb=" CG ASP A 395 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.42 -11.12 2.00e+00 2.50e-01 3.09e+01 angle pdb=" N PHE A 53 " pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 111.36 105.81 5.55 1.09e+00 8.42e-01 2.59e+01 angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 120.85 115.79 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.58 -8.08 1.70e+00 3.46e-01 2.26e+01 ... (remaining 5977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2177 17.95 - 35.90: 257 35.90 - 53.86: 63 53.86 - 71.81: 15 71.81 - 89.76: 6 Dihedral angle restraints: 2518 sinusoidal: 995 harmonic: 1523 Sorted by residual: dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -49.63 -36.37 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 663 0.277 - 0.554: 1 0.554 - 0.831: 0 0.831 - 1.108: 0 1.108 - 1.385: 2 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.80e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.54e+01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 663 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.101 2.00e-02 2.50e+03 1.71e-01 3.66e+02 pdb=" CG ASN A 181 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.307 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.134 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" CG ASN A 184 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.203 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.064 2.00e-02 2.50e+03 6.39e-02 5.11e+01 pdb=" CG ASN A 176 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.098 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.077 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 40 2.51 - 3.10: 3259 3.10 - 3.70: 7029 3.70 - 4.30: 10384 4.30 - 4.90: 16710 Nonbonded interactions: 37422 Sorted by model distance: nonbonded pdb=" O HOH A 805 " pdb=" O HOH A 828 " model vdw 1.907 3.040 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 806 " model vdw 2.000 3.040 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 2.008 3.040 nonbonded pdb=" O LEU A 298 " pdb=" O HOH A 802 " model vdw 2.030 3.040 nonbonded pdb=" OG1 THR A 290 " pdb=" O HOH A 803 " model vdw 2.045 3.040 ... (remaining 37417 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: 0.390 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.660 Find NCS groups from input model: 0.040 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 0.072 4393 Z= 0.357 Angle : 0.777 11.117 5982 Z= 0.474 Chirality : 0.084 1.385 666 Planarity : 0.005 0.042 725 Dihedral : 17.204 89.759 1549 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 26.73 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.36), residues: 527 helix: 0.63 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -1.32 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 500 HIS 0.007 0.002 HIS A 198 PHE 0.026 0.003 PHE A 398 TYR 0.020 0.002 TYR A 72 ARG 0.007 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.498 Fit side-chains REVERT: A 51 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6421 (p90) REVERT: A 121 MET cc_start: 0.8983 (ptm) cc_final: 0.8730 (ptp) REVERT: A 163 GLN cc_start: 0.8134 (mt0) cc_final: 0.7193 (pm20) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 1.2324 time to fit residues: 83.3307 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 338 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 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 153 ASN A 163 GLN A 198 HIS A 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4393 Z= 0.207 Angle : 0.615 8.889 5982 Z= 0.318 Chirality : 0.045 0.355 666 Planarity : 0.004 0.040 725 Dihedral : 6.838 58.552 643 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.68 % Allowed : 20.71 % Favored : 74.61 % 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: 0.98 (0.37), residues: 527 helix: 1.41 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.003 0.001 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.020 0.002 TYR A 72 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.450 Fit side-chains REVERT: A 72 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.7922 (p90) REVERT: A 163 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: A 560 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6667 (mttm) REVERT: A 572 GLN cc_start: 0.6045 (OUTLIER) cc_final: 0.5769 (mm110) outliers start: 21 outliers final: 10 residues processed: 73 average time/residue: 1.1662 time to fit residues: 88.8762 Evaluate side-chains 64 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 572 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4393 Z= 0.212 Angle : 0.592 7.940 5982 Z= 0.308 Chirality : 0.046 0.335 666 Planarity : 0.004 0.039 725 Dihedral : 6.082 48.462 641 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.35 % Allowed : 20.04 % Favored : 74.61 % 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: 1.20 (0.36), residues: 527 helix: 1.63 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.41 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.022 0.002 TYR A 72 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.469 Fit side-chains REVERT: A 72 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8009 (p90) outliers start: 24 outliers final: 16 residues processed: 73 average time/residue: 0.9495 time to fit residues: 72.8364 Evaluate side-chains 69 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 0.0010 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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: 0.8272 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4393 Z= 0.181 Angle : 0.540 7.940 5982 Z= 0.283 Chirality : 0.044 0.278 666 Planarity : 0.004 0.037 725 Dihedral : 5.304 30.940 641 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.45 % Allowed : 21.16 % Favored : 74.39 % 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 (0.37), residues: 527 helix: 1.80 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.019 0.002 TYR A 72 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.444 Fit side-chains REVERT: A 72 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.7930 (p90) outliers start: 20 outliers final: 11 residues processed: 72 average time/residue: 0.9782 time to fit residues: 73.8191 Evaluate side-chains 63 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 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: 0.8256 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4393 Z= 0.168 Angle : 0.516 7.721 5982 Z= 0.271 Chirality : 0.043 0.261 666 Planarity : 0.004 0.036 725 Dihedral : 4.789 31.374 641 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.23 % Allowed : 21.16 % Favored : 74.61 % 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: 1.65 (0.37), residues: 527 helix: 1.95 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.27 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.018 0.001 TYR A 72 ARG 0.005 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.788 Fit side-chains REVERT: A 72 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8007 (p90) REVERT: A 402 GLU cc_start: 0.7840 (tp30) cc_final: 0.7586 (tp30) outliers start: 19 outliers final: 15 residues processed: 73 average time/residue: 0.9063 time to fit residues: 69.7461 Evaluate side-chains 69 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4393 Z= 0.184 Angle : 0.528 7.644 5982 Z= 0.277 Chirality : 0.043 0.255 666 Planarity : 0.004 0.036 725 Dihedral : 4.786 31.909 641 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.23 % Allowed : 21.83 % Favored : 73.94 % 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: 1.65 (0.37), residues: 527 helix: 1.94 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.020 0.002 TYR A 72 ARG 0.004 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.492 Fit side-chains REVERT: A 72 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.7977 (p90) REVERT: A 402 GLU cc_start: 0.7838 (tp30) cc_final: 0.7578 (tp30) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 0.9499 time to fit residues: 71.7743 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4393 Z= 0.187 Angle : 0.528 7.603 5982 Z= 0.278 Chirality : 0.043 0.242 666 Planarity : 0.004 0.036 725 Dihedral : 4.762 32.128 641 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.79 % Allowed : 22.05 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.37), residues: 527 helix: 1.93 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.23 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.021 0.002 TYR A 72 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.439 Fit side-chains REVERT: A 72 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7983 (p90) REVERT: A 250 MET cc_start: 0.7899 (mmt) cc_final: 0.7678 (mmm) REVERT: A 402 GLU cc_start: 0.7841 (tp30) cc_final: 0.7574 (tp30) outliers start: 17 outliers final: 14 residues processed: 68 average time/residue: 0.9788 time to fit residues: 69.9140 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 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 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4393 Z= 0.173 Angle : 0.528 7.529 5982 Z= 0.278 Chirality : 0.043 0.231 666 Planarity : 0.004 0.036 725 Dihedral : 4.663 32.176 641 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.79 % Allowed : 22.05 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.37), residues: 527 helix: 1.97 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.22 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.019 0.002 TYR A 72 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.502 Fit side-chains REVERT: A 72 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.7910 (p90) REVERT: A 402 GLU cc_start: 0.7836 (tp30) cc_final: 0.7565 (tp30) outliers start: 17 outliers final: 15 residues processed: 70 average time/residue: 1.0103 time to fit residues: 74.1813 Evaluate side-chains 70 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4393 Z= 0.150 Angle : 0.509 7.556 5982 Z= 0.267 Chirality : 0.042 0.260 666 Planarity : 0.004 0.035 725 Dihedral : 4.470 31.643 641 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.56 % Allowed : 22.05 % Favored : 74.39 % 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: 1.87 (0.37), residues: 527 helix: 2.10 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.14 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.002 0.001 HIS A 198 PHE 0.030 0.001 PHE A 398 TYR 0.016 0.001 TYR A 72 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.517 Fit side-chains REVERT: A 72 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7874 (p90) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 1.0656 time to fit residues: 79.1564 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4393 Z= 0.181 Angle : 0.529 7.427 5982 Z= 0.279 Chirality : 0.043 0.235 666 Planarity : 0.004 0.036 725 Dihedral : 4.555 32.366 641 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.90 % Allowed : 22.72 % Favored : 74.39 % 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: 1.81 (0.37), residues: 527 helix: 2.03 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.13 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.021 0.002 TYR A 72 ARG 0.003 0.000 ARG A 566 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.731 Fit side-chains REVERT: A 72 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7985 (p90) outliers start: 13 outliers final: 11 residues processed: 65 average time/residue: 1.0255 time to fit residues: 69.9439 Evaluate side-chains 65 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.093809 restraints weight = 4617.751| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.47 r_work: 0.2916 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4393 Z= 0.158 Angle : 0.519 7.439 5982 Z= 0.271 Chirality : 0.042 0.229 666 Planarity : 0.004 0.036 725 Dihedral : 4.461 31.944 641 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.12 % Allowed : 22.49 % Favored : 74.39 % 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: 1.86 (0.37), residues: 527 helix: 2.07 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.14 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.017 0.001 TYR A 72 ARG 0.003 0.000 ARG A 566 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1933.03 seconds wall clock time: 35 minutes 34.87 seconds (2134.87 seconds total)