Starting phenix.real_space_refine on Wed Jan 17 14:55:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/01_2024/8org_17123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/01_2024/8org_17123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/01_2024/8org_17123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/01_2024/8org_17123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/01_2024/8org_17123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/01_2024/8org_17123.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1206 2.51 5 N 357 2.21 5 O 372 1.98 5 H 2025 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3966 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1322 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "A" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1322 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "C" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1322 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Time building chain proxies: 2.16, per 1000 atoms: 0.54 Number of scatterers: 3966 At special positions: 0 Unit cell: (70.8825, 92.6925, 35.9865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 372 8.00 N 357 7.00 C 1206 6.00 H 2025 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 538.0 milliseconds 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 456 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 283 removed outlier: 6.401A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 299 removed outlier: 6.398A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 310 removed outlier: 6.827A pdb=" N GLY B 304 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY B 303 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL C 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER B 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE C 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 318 removed outlier: 6.459A pdb=" N ASP B 314 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LYS A 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER B 316 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N SER C 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 315 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL C 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.760A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.457A pdb=" N ASN B 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS C 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS B 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 341 removed outlier: 6.392A pdb=" N VAL B 337 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS A 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 339 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.729A pdb=" N ILE B 360 " --> pdb=" O THR A 361 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 126 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: 1.30 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 2019 1.03 - 1.22: 6 1.22 - 1.41: 755 1.41 - 1.61: 1204 1.61 - 1.80: 6 Bond restraints: 3990 Sorted by residual: bond pdb=" CB PRO C 312 " pdb=" CG PRO C 312 " ideal model delta sigma weight residual 1.492 1.411 0.081 5.00e-02 4.00e+02 2.62e+00 bond pdb=" CB PRO B 312 " pdb=" CG PRO B 312 " ideal model delta sigma weight residual 1.492 1.411 0.081 5.00e-02 4.00e+02 2.59e+00 bond pdb=" CB PRO A 312 " pdb=" CG PRO A 312 " ideal model delta sigma weight residual 1.492 1.412 0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" CE LYS C 311 " pdb=" NZ LYS C 311 " ideal model delta sigma weight residual 1.489 1.442 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CE LYS A 311 " pdb=" NZ LYS A 311 " ideal model delta sigma weight residual 1.489 1.443 0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 3985 not shown) Histogram of bond angle deviations from ideal: 102.70 - 108.45: 1562 108.45 - 114.20: 3825 114.20 - 119.94: 630 119.94 - 125.69: 1185 125.69 - 131.44: 79 Bond angle restraints: 7281 Sorted by residual: angle pdb=" CA LYS C 281 " pdb=" CB LYS C 281 " pdb=" CG LYS C 281 " ideal model delta sigma weight residual 114.10 120.92 -6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA LYS A 281 " pdb=" CB LYS A 281 " pdb=" CG LYS A 281 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA LYS B 281 " pdb=" CB LYS B 281 " pdb=" CG LYS B 281 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N LYS A 281 " pdb=" CA LYS A 281 " pdb=" C LYS A 281 " ideal model delta sigma weight residual 109.23 114.31 -5.08 1.55e+00 4.16e-01 1.08e+01 angle pdb=" N LYS B 281 " pdb=" CA LYS B 281 " pdb=" C LYS B 281 " ideal model delta sigma weight residual 109.23 114.30 -5.07 1.55e+00 4.16e-01 1.07e+01 ... (remaining 7276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 1563 13.45 - 26.91: 143 26.91 - 40.36: 19 40.36 - 53.81: 12 53.81 - 67.26: 39 Dihedral angle restraints: 1776 sinusoidal: 999 harmonic: 777 Sorted by residual: dihedral pdb=" CA LEU A 357 " pdb=" C LEU A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU B 357 " pdb=" C LEU B 357 " pdb=" N ASP B 358 " pdb=" CA ASP B 358 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LEU C 357 " pdb=" C LEU C 357 " pdb=" N ASP C 358 " pdb=" CA ASP C 358 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 1773 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.076: 228 0.076 - 0.152: 63 0.152 - 0.227: 3 0.227 - 0.303: 3 0.303 - 0.378: 3 Chirality restraints: 300 Sorted by residual: chirality pdb=" CB ILE B 360 " pdb=" CA ILE B 360 " pdb=" CG1 ILE B 360 " pdb=" CG2 ILE B 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB ILE C 360 " pdb=" CA ILE C 360 " pdb=" CG1 ILE C 360 " pdb=" CG2 ILE C 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB ILE A 360 " pdb=" CA ILE A 360 " pdb=" CG1 ILE A 360 " pdb=" CG2 ILE A 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 297 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 288 " -0.025 2.00e-02 2.50e+03 3.22e-02 1.55e+01 pdb=" CD GLN B 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN B 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN B 288 " 0.053 2.00e-02 2.50e+03 pdb="HE21 GLN B 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN B 288 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 288 " -0.025 2.00e-02 2.50e+03 3.21e-02 1.55e+01 pdb=" CD GLN A 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN A 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 288 " 0.054 2.00e-02 2.50e+03 pdb="HE21 GLN A 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 288 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 288 " -0.025 2.00e-02 2.50e+03 3.20e-02 1.53e+01 pdb=" CD GLN C 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN C 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN C 288 " 0.053 2.00e-02 2.50e+03 pdb="HE21 GLN C 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN C 288 " -0.049 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1175 2.32 - 2.89: 9040 2.89 - 3.46: 8824 3.46 - 4.03: 13749 4.03 - 4.60: 19241 Nonbonded interactions: 52029 Sorted by model distance: nonbonded pdb=" OD2 ASP C 295 " pdb=" HZ3 LYS C 311 " model vdw 1.746 1.850 nonbonded pdb=" OD2 ASP B 295 " pdb=" HZ3 LYS B 311 " model vdw 1.747 1.850 nonbonded pdb=" OD2 ASP A 295 " pdb=" HZ3 LYS A 311 " model vdw 1.748 1.850 nonbonded pdb="HD22 ASN A 296 " pdb=" OD2 ASP A 358 " model vdw 1.764 1.850 nonbonded pdb="HD22 ASN B 296 " pdb=" OD2 ASP B 358 " model vdw 1.765 1.850 ... (remaining 52024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.190 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: 0.070 Extract box with map and model: 3.680 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.230 Find NCS groups from input model: 0.150 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.010 0.081 1965 Z= 0.651 Angle : 1.263 7.621 2628 Z= 0.667 Chirality : 0.075 0.378 300 Planarity : 0.005 0.032 336 Dihedral : 11.917 66.727 759 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.43), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.006 HIS A 299 PHE 0.012 0.005 PHE C 346 TYR 0.016 0.009 TYR A 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 281 LYS cc_start: 0.7478 (ptpt) cc_final: 0.7251 (ptmt) REVERT: B 317 LYS cc_start: 0.8471 (tttt) cc_final: 0.8201 (tttm) REVERT: B 331 LYS cc_start: 0.8517 (mttt) cc_final: 0.8284 (mttt) REVERT: B 341 SER cc_start: 0.8619 (m) cc_final: 0.8368 (t) REVERT: A 281 LYS cc_start: 0.8333 (ptpt) cc_final: 0.8063 (ptmt) REVERT: A 340 LYS cc_start: 0.8368 (mttt) cc_final: 0.8123 (mtpp) REVERT: A 349 ARG cc_start: 0.7520 (mtt180) cc_final: 0.5917 (mmp-170) REVERT: A 351 GLN cc_start: 0.7767 (tt0) cc_final: 0.7484 (tt0) REVERT: A 356 SER cc_start: 0.8520 (t) cc_final: 0.8006 (p) REVERT: A 358 ASP cc_start: 0.7114 (t0) cc_final: 0.6881 (t0) REVERT: C 314 ASP cc_start: 0.7593 (t0) cc_final: 0.7113 (t0) REVERT: C 331 LYS cc_start: 0.8541 (mttt) cc_final: 0.8314 (mttt) REVERT: C 338 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7337 (mp0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 2.5043 time to fit residues: 244.2372 Evaluate side-chains 58 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN A 286 ASN A 336 GLN A 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1965 Z= 0.192 Angle : 0.579 4.266 2628 Z= 0.293 Chirality : 0.051 0.140 300 Planarity : 0.003 0.019 336 Dihedral : 6.648 17.152 261 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.39 % Allowed : 14.04 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 299 PHE 0.004 0.001 PHE C 346 TYR 0.003 0.001 TYR A 310 ARG 0.002 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.303 Fit side-chains REVERT: B 317 LYS cc_start: 0.8401 (tttt) cc_final: 0.8174 (tttm) REVERT: B 341 SER cc_start: 0.8432 (m) cc_final: 0.8194 (t) REVERT: A 340 LYS cc_start: 0.8362 (mttt) cc_final: 0.8067 (mtpp) REVERT: A 349 ARG cc_start: 0.7519 (mtt180) cc_final: 0.6241 (mtt-85) REVERT: C 317 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8619 (tptm) REVERT: C 338 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7326 (mp0) REVERT: C 340 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8255 (mtpm) outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 1.8809 time to fit residues: 138.3699 Evaluate side-chains 60 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN A 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1965 Z= 0.231 Angle : 0.547 4.520 2628 Z= 0.279 Chirality : 0.051 0.129 300 Planarity : 0.003 0.027 336 Dihedral : 6.058 16.590 261 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.51 % Allowed : 17.98 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.42), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.003 0.001 PHE C 346 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.344 Fit side-chains REVERT: B 317 LYS cc_start: 0.8388 (tttt) cc_final: 0.8129 (tttm) REVERT: B 341 SER cc_start: 0.8515 (m) cc_final: 0.8292 (t) REVERT: A 336 GLN cc_start: 0.7906 (mt0) cc_final: 0.7538 (tt0) REVERT: A 340 LYS cc_start: 0.8288 (mttt) cc_final: 0.8051 (mtpp) REVERT: A 349 ARG cc_start: 0.7811 (mtt180) cc_final: 0.5891 (mmp-170) REVERT: A 351 GLN cc_start: 0.7955 (mt0) cc_final: 0.7702 (mt0) REVERT: C 338 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7303 (mp0) REVERT: C 340 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8322 (mtpm) outliers start: 8 outliers final: 2 residues processed: 58 average time/residue: 1.4991 time to fit residues: 89.4279 Evaluate side-chains 56 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1965 Z= 0.143 Angle : 0.478 3.613 2628 Z= 0.245 Chirality : 0.051 0.128 300 Planarity : 0.003 0.028 336 Dihedral : 5.369 14.958 261 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.07 % Allowed : 19.30 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.42), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 PHE 0.001 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8388 (tttt) cc_final: 0.8143 (tttm) REVERT: B 341 SER cc_start: 0.8595 (m) cc_final: 0.8353 (t) REVERT: A 340 LYS cc_start: 0.8330 (mttt) cc_final: 0.8069 (mtpp) REVERT: A 349 ARG cc_start: 0.7749 (mtt180) cc_final: 0.5820 (mmp-170) REVERT: A 351 GLN cc_start: 0.7950 (mt0) cc_final: 0.7709 (mt0) REVERT: C 317 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8633 (tptm) REVERT: C 338 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7318 (mp0) REVERT: C 340 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8259 (mtpm) outliers start: 7 outliers final: 2 residues processed: 56 average time/residue: 1.5804 time to fit residues: 90.9693 Evaluate side-chains 54 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN A 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1965 Z= 0.177 Angle : 0.476 3.628 2628 Z= 0.245 Chirality : 0.051 0.125 300 Planarity : 0.003 0.030 336 Dihedral : 5.307 14.944 261 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 21.05 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.43), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8373 (tttt) cc_final: 0.8119 (tttm) REVERT: B 341 SER cc_start: 0.8576 (m) cc_final: 0.8303 (t) REVERT: A 340 LYS cc_start: 0.8331 (mttt) cc_final: 0.8059 (mtpp) REVERT: A 349 ARG cc_start: 0.7830 (mtt180) cc_final: 0.5858 (mmp-170) REVERT: A 351 GLN cc_start: 0.7960 (mt0) cc_final: 0.7718 (mt0) REVERT: C 338 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7339 (mp0) outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 1.5510 time to fit residues: 81.3645 Evaluate side-chains 51 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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: 0.7593 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1965 Z= 0.131 Angle : 0.455 3.480 2628 Z= 0.231 Chirality : 0.051 0.124 300 Planarity : 0.003 0.029 336 Dihedral : 4.908 14.505 261 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.75 % Allowed : 19.74 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.43), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8394 (tttt) cc_final: 0.8156 (tttm) REVERT: B 341 SER cc_start: 0.8546 (m) cc_final: 0.8279 (t) REVERT: A 340 LYS cc_start: 0.8348 (mttt) cc_final: 0.8062 (mtpp) REVERT: A 349 ARG cc_start: 0.7811 (mtt180) cc_final: 0.6388 (mtt-85) REVERT: A 351 GLN cc_start: 0.7975 (mt0) cc_final: 0.7751 (mt0) REVERT: C 317 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8619 (tptm) REVERT: C 338 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7336 (mp0) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 1.5787 time to fit residues: 85.9713 Evaluate side-chains 52 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain C residue 317 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN A 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1965 Z= 0.179 Angle : 0.473 3.875 2628 Z= 0.241 Chirality : 0.050 0.122 300 Planarity : 0.003 0.030 336 Dihedral : 5.021 14.655 261 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.63 % Allowed : 19.74 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.44), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 299 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8398 (tttt) cc_final: 0.8161 (tttm) REVERT: B 341 SER cc_start: 0.8558 (m) cc_final: 0.8293 (t) REVERT: A 325 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 340 LYS cc_start: 0.8338 (mttt) cc_final: 0.8059 (mtpp) REVERT: A 349 ARG cc_start: 0.7857 (mtt180) cc_final: 0.5924 (mmp-170) REVERT: A 351 GLN cc_start: 0.7951 (mt0) cc_final: 0.7738 (mt0) REVERT: C 317 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8619 (tptm) REVERT: C 338 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7358 (mp0) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 1.5324 time to fit residues: 79.0281 Evaluate side-chains 50 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 317 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7605 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1965 Z= 0.143 Angle : 0.453 3.709 2628 Z= 0.230 Chirality : 0.050 0.122 300 Planarity : 0.003 0.029 336 Dihedral : 4.835 14.465 261 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.32 % Allowed : 20.61 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.44), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8395 (tttt) cc_final: 0.8167 (tttm) REVERT: B 341 SER cc_start: 0.8558 (m) cc_final: 0.8291 (t) REVERT: A 340 LYS cc_start: 0.8344 (mttt) cc_final: 0.8067 (mtpp) REVERT: A 349 ARG cc_start: 0.7848 (mtt180) cc_final: 0.5856 (mmp-170) REVERT: A 351 GLN cc_start: 0.8007 (mt0) cc_final: 0.7686 (mt0) REVERT: C 317 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8625 (tptm) REVERT: C 338 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7346 (mp0) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 1.5135 time to fit residues: 73.2721 Evaluate side-chains 47 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain C residue 317 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.0470 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1965 Z= 0.131 Angle : 0.447 3.792 2628 Z= 0.227 Chirality : 0.051 0.122 300 Planarity : 0.003 0.029 336 Dihedral : 4.641 14.225 261 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.32 % Allowed : 21.05 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.45), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8396 (tttt) cc_final: 0.8179 (tttm) REVERT: B 341 SER cc_start: 0.8559 (m) cc_final: 0.8313 (t) REVERT: A 340 LYS cc_start: 0.8355 (mttt) cc_final: 0.8070 (mtpp) REVERT: A 349 ARG cc_start: 0.7828 (mtt180) cc_final: 0.6348 (mtt-85) REVERT: A 351 GLN cc_start: 0.8015 (mt0) cc_final: 0.7711 (mt0) REVERT: C 317 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8623 (tptm) REVERT: C 338 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7339 (mp0) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 1.4923 time to fit residues: 72.2804 Evaluate side-chains 45 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain C residue 317 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.7580 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1965 Z= 0.131 Angle : 0.442 3.653 2628 Z= 0.223 Chirality : 0.051 0.122 300 Planarity : 0.003 0.030 336 Dihedral : 4.579 14.089 261 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.88 % Allowed : 21.49 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.45), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8389 (tttt) cc_final: 0.8161 (tttm) REVERT: B 341 SER cc_start: 0.8582 (m) cc_final: 0.8313 (t) REVERT: A 340 LYS cc_start: 0.8361 (mttt) cc_final: 0.8073 (mtpp) REVERT: A 349 ARG cc_start: 0.7821 (mtt180) cc_final: 0.6343 (mtt-85) REVERT: A 351 GLN cc_start: 0.8022 (mt0) cc_final: 0.7718 (mt0) REVERT: C 317 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8625 (tptm) REVERT: C 338 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7335 (mp0) REVERT: C 351 GLN cc_start: 0.7810 (tt0) cc_final: 0.7555 (mt0) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 1.6443 time to fit residues: 79.3939 Evaluate side-chains 46 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain C residue 317 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.146081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.128820 restraints weight = 7034.043| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.87 r_work: 0.3986 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1965 Z= 0.128 Angle : 0.441 3.803 2628 Z= 0.222 Chirality : 0.051 0.122 300 Planarity : 0.003 0.029 336 Dihedral : 4.532 14.026 261 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 21.49 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.45), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 PHE 0.002 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3290.91 seconds wall clock time: 60 minutes 13.34 seconds (3613.34 seconds total)