Starting phenix.real_space_refine on Wed Nov 13 23:22:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg6_51325/11_2024/9gg6_51325_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg6_51325/11_2024/9gg6_51325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg6_51325/11_2024/9gg6_51325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg6_51325/11_2024/9gg6_51325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg6_51325/11_2024/9gg6_51325_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg6_51325/11_2024/9gg6_51325_neut.cif" } resolution = 3.36 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1329 2.51 5 N 396 2.21 5 O 411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2142 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Restraints were copied for chains: C, B Time building chain proxies: 2.63, per 1000 atoms: 1.23 Number of scatterers: 2142 At special positions: 0 Unit cell: (117.008, 66.744, 35.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 411 8.00 N 396 7.00 C 1329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 361.0 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 498 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 717 1.34 - 1.46: 294 1.46 - 1.57: 1152 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 2169 Sorted by residual: bond pdb=" C GLY C 273 " pdb=" O GLY C 273 " ideal model delta sigma weight residual 1.243 1.234 0.009 9.30e-03 1.16e+04 9.51e-01 bond pdb=" C GLY A 273 " pdb=" O GLY A 273 " ideal model delta sigma weight residual 1.243 1.234 0.009 9.30e-03 1.16e+04 9.37e-01 bond pdb=" C GLY B 273 " pdb=" O GLY B 273 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 7.36e-01 bond pdb=" CA LYS C 294 " pdb=" C LYS C 294 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.34e-02 5.57e+03 4.17e-01 bond pdb=" CA LYS B 294 " pdb=" C LYS B 294 " ideal model delta sigma weight residual 1.523 1.532 -0.008 1.34e-02 5.57e+03 3.95e-01 ... (remaining 2164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 2860 2.18 - 4.37: 38 4.37 - 6.55: 3 6.55 - 8.73: 0 8.73 - 10.92: 3 Bond angle restraints: 2904 Sorted by residual: angle pdb=" CA LEU C 315 " pdb=" CB LEU C 315 " pdb=" CG LEU C 315 " ideal model delta sigma weight residual 116.30 127.22 -10.92 3.50e+00 8.16e-02 9.73e+00 angle pdb=" CA LEU B 315 " pdb=" CB LEU B 315 " pdb=" CG LEU B 315 " ideal model delta sigma weight residual 116.30 127.17 -10.87 3.50e+00 8.16e-02 9.64e+00 angle pdb=" CA LEU A 315 " pdb=" CB LEU A 315 " pdb=" CG LEU A 315 " ideal model delta sigma weight residual 116.30 127.16 -10.86 3.50e+00 8.16e-02 9.63e+00 angle pdb=" C LYS C 294 " pdb=" N ASP C 295 " pdb=" CA ASP C 295 " ideal model delta sigma weight residual 120.90 124.21 -3.31 1.41e+00 5.03e-01 5.52e+00 angle pdb=" C LYS A 294 " pdb=" N ASP A 295 " pdb=" CA ASP A 295 " ideal model delta sigma weight residual 120.90 124.21 -3.31 1.41e+00 5.03e-01 5.50e+00 ... (remaining 2899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1183 17.73 - 35.47: 110 35.47 - 53.20: 36 53.20 - 70.94: 3 70.94 - 88.67: 3 Dihedral angle restraints: 1335 sinusoidal: 549 harmonic: 786 Sorted by residual: dihedral pdb=" CB LYS A 331 " pdb=" CG LYS A 331 " pdb=" CD LYS A 331 " pdb=" CE LYS A 331 " ideal model delta sinusoidal sigma weight residual 180.00 124.11 55.89 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CB LYS C 331 " pdb=" CG LYS C 331 " pdb=" CD LYS C 331 " pdb=" CE LYS C 331 " ideal model delta sinusoidal sigma weight residual 180.00 124.14 55.86 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CB LYS B 331 " pdb=" CG LYS B 331 " pdb=" CD LYS B 331 " pdb=" CE LYS B 331 " ideal model delta sinusoidal sigma weight residual 180.00 124.19 55.81 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 196 0.030 - 0.059: 65 0.059 - 0.089: 12 0.089 - 0.118: 51 0.118 - 0.148: 6 Chirality restraints: 330 Sorted by residual: chirality pdb=" CG LEU A 315 " pdb=" CB LEU A 315 " pdb=" CD1 LEU A 315 " pdb=" CD2 LEU A 315 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CG LEU B 315 " pdb=" CB LEU B 315 " pdb=" CD1 LEU B 315 " pdb=" CD2 LEU B 315 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CG LEU C 315 " pdb=" CB LEU C 315 " pdb=" CD1 LEU C 315 " pdb=" CD2 LEU C 315 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 327 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 364 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 363 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO C 364 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 364 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 364 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 363 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO B 364 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " 0.018 5.00e-02 4.00e+02 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 790 2.89 - 3.39: 1604 3.39 - 3.89: 3569 3.89 - 4.40: 3374 4.40 - 4.90: 7229 Nonbonded interactions: 16566 Sorted by model distance: nonbonded pdb=" NZ LYS A 281 " pdb=" OD2 ASP C 348 " model vdw 2.386 3.120 nonbonded pdb=" OD2 ASP A 348 " pdb=" NZ LYS B 281 " model vdw 2.387 3.120 nonbonded pdb=" N ASP C 295 " pdb=" OD1 ASP C 295 " model vdw 2.404 3.120 nonbonded pdb=" N ASP B 295 " pdb=" OD1 ASP B 295 " model vdw 2.404 3.120 nonbonded pdb=" N ASP A 295 " pdb=" OD1 ASP A 295 " model vdw 2.405 3.120 ... (remaining 16561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.900 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2169 Z= 0.136 Angle : 0.710 10.918 2904 Z= 0.346 Chirality : 0.051 0.148 330 Planarity : 0.004 0.032 375 Dihedral : 15.584 88.671 837 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 26.51 % Favored : 73.49 % 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: -3.00 (0.41), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.008 0.003 PHE A 346 TYR 0.003 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.236 Fit side-chains REVERT: A 294 LYS cc_start: 0.8025 (mttt) cc_final: 0.7709 (tttt) REVERT: A 317 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7716 (tttm) REVERT: A 321 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6828 (mmmm) REVERT: B 294 LYS cc_start: 0.8088 (mttt) cc_final: 0.7372 (pttm) REVERT: B 317 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8238 (tttm) REVERT: B 321 LYS cc_start: 0.7489 (mmtt) cc_final: 0.5954 (pttp) REVERT: C 294 LYS cc_start: 0.7979 (mttt) cc_final: 0.7769 (tttt) REVERT: C 321 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6658 (mmmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2687 time to fit residues: 16.4024 Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2169 Z= 0.242 Angle : 0.623 8.219 2904 Z= 0.306 Chirality : 0.050 0.133 330 Planarity : 0.004 0.041 375 Dihedral : 4.352 10.517 291 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 7.23 % Allowed : 20.88 % Favored : 71.89 % 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: -2.68 (0.44), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 329 PHE 0.009 0.002 PHE A 346 TYR 0.007 0.002 TYR C 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.272 Fit side-chains REVERT: A 294 LYS cc_start: 0.7852 (mttt) cc_final: 0.7534 (tttt) REVERT: A 351 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: B 294 LYS cc_start: 0.7920 (mttt) cc_final: 0.7211 (pttm) REVERT: B 321 LYS cc_start: 0.7720 (mmtt) cc_final: 0.6067 (pttm) REVERT: B 351 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: C 294 LYS cc_start: 0.7845 (mttt) cc_final: 0.7573 (tttt) REVERT: C 340 LYS cc_start: 0.8338 (mptt) cc_final: 0.8138 (mptt) REVERT: C 342 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8204 (mt-10) REVERT: C 351 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7821 (pt0) outliers start: 18 outliers final: 13 residues processed: 51 average time/residue: 0.2418 time to fit residues: 13.6473 Evaluate side-chains 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 351 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.0060 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2169 Z= 0.105 Angle : 0.484 6.537 2904 Z= 0.235 Chirality : 0.050 0.124 330 Planarity : 0.003 0.022 375 Dihedral : 3.892 12.057 291 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 6.43 % Allowed : 24.50 % Favored : 69.08 % 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: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 PHE 0.005 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.270 Fit side-chains REVERT: A 294 LYS cc_start: 0.7806 (mttt) cc_final: 0.7491 (tttt) REVERT: B 294 LYS cc_start: 0.7825 (mttt) cc_final: 0.7068 (pttm) REVERT: B 321 LYS cc_start: 0.7564 (mmtt) cc_final: 0.6022 (pttp) REVERT: B 349 ARG cc_start: 0.8754 (ttm170) cc_final: 0.8491 (ttm170) REVERT: B 351 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8124 (pt0) REVERT: C 294 LYS cc_start: 0.7729 (mttt) cc_final: 0.7476 (tttt) REVERT: C 342 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8246 (mt-10) outliers start: 16 outliers final: 13 residues processed: 54 average time/residue: 0.2305 time to fit residues: 13.8535 Evaluate side-chains 54 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 0.0770 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.0070 chunk 0 optimal weight: 7.9990 overall best weight: 3.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2169 Z= 0.225 Angle : 0.593 6.654 2904 Z= 0.293 Chirality : 0.050 0.127 330 Planarity : 0.004 0.035 375 Dihedral : 4.253 11.952 291 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 7.23 % Allowed : 23.69 % Favored : 69.08 % 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: -2.44 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.006 0.002 PHE A 346 TYR 0.007 0.002 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.263 Fit side-chains REVERT: A 294 LYS cc_start: 0.7915 (mttt) cc_final: 0.7580 (tttt) REVERT: B 294 LYS cc_start: 0.8057 (mttt) cc_final: 0.7357 (pttm) REVERT: B 321 LYS cc_start: 0.7963 (mmtt) cc_final: 0.6230 (pttp) REVERT: B 351 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: C 294 LYS cc_start: 0.7790 (mttt) cc_final: 0.7529 (tttt) REVERT: C 342 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8299 (mt-10) REVERT: C 351 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7654 (pt0) outliers start: 18 outliers final: 14 residues processed: 50 average time/residue: 0.2278 time to fit residues: 12.6905 Evaluate side-chains 50 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2169 Z= 0.127 Angle : 0.517 7.459 2904 Z= 0.253 Chirality : 0.050 0.122 330 Planarity : 0.003 0.028 375 Dihedral : 4.075 12.681 291 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.83 % Allowed : 24.90 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.005 0.002 PHE A 346 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.264 Fit side-chains REVERT: A 290 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7519 (mttt) REVERT: A 294 LYS cc_start: 0.7906 (mttt) cc_final: 0.7597 (tttt) REVERT: B 294 LYS cc_start: 0.7922 (mttt) cc_final: 0.7207 (pttm) REVERT: B 321 LYS cc_start: 0.7882 (mmtt) cc_final: 0.6199 (pttp) REVERT: B 351 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: C 294 LYS cc_start: 0.7718 (mttt) cc_final: 0.7488 (tttt) REVERT: C 342 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8266 (mt-10) outliers start: 17 outliers final: 15 residues processed: 51 average time/residue: 0.2291 time to fit residues: 12.9694 Evaluate side-chains 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 overall best weight: 1.4680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 307 GLN B 299 HIS B 307 GLN C 288 GLN C 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2169 Z= 0.128 Angle : 0.516 6.579 2904 Z= 0.252 Chirality : 0.050 0.121 330 Planarity : 0.003 0.029 375 Dihedral : 3.981 13.633 291 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 7.23 % Allowed : 24.10 % Favored : 68.67 % 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: -2.26 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.005 0.002 PHE A 346 TYR 0.004 0.001 TYR B 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.259 Fit side-chains REVERT: A 294 LYS cc_start: 0.7911 (mttt) cc_final: 0.7589 (tttt) REVERT: A 340 LYS cc_start: 0.8506 (mptt) cc_final: 0.8281 (mmtm) REVERT: B 294 LYS cc_start: 0.7958 (mttt) cc_final: 0.7262 (pttm) REVERT: B 321 LYS cc_start: 0.7895 (mmtt) cc_final: 0.6187 (pttp) REVERT: C 295 ASP cc_start: 0.7824 (p0) cc_final: 0.7555 (p0) REVERT: C 342 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8301 (mt-10) outliers start: 18 outliers final: 16 residues processed: 53 average time/residue: 0.2412 time to fit residues: 14.2374 Evaluate side-chains 54 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.0870 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 0.0030 chunk 24 optimal weight: 5.9990 overall best weight: 2.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2169 Z= 0.172 Angle : 0.542 6.967 2904 Z= 0.265 Chirality : 0.050 0.124 330 Planarity : 0.004 0.033 375 Dihedral : 4.186 13.904 291 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 7.63 % Allowed : 23.29 % Favored : 69.08 % 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: -2.22 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 299 PHE 0.005 0.002 PHE A 346 TYR 0.006 0.002 TYR B 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.260 Fit side-chains REVERT: A 294 LYS cc_start: 0.7980 (mttt) cc_final: 0.7633 (tttt) REVERT: B 294 LYS cc_start: 0.8062 (mttt) cc_final: 0.7373 (pttm) REVERT: B 321 LYS cc_start: 0.8029 (mmtt) cc_final: 0.6268 (pttp) REVERT: B 351 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: C 295 ASP cc_start: 0.7967 (p0) cc_final: 0.7652 (p0) REVERT: C 342 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 351 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7684 (pt0) outliers start: 19 outliers final: 15 residues processed: 52 average time/residue: 0.2214 time to fit residues: 13.0030 Evaluate side-chains 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 351 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8494 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2169 Z= 0.098 Angle : 0.500 7.719 2904 Z= 0.240 Chirality : 0.050 0.123 330 Planarity : 0.003 0.026 375 Dihedral : 3.981 14.295 291 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 6.83 % Allowed : 24.50 % Favored : 68.67 % 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: -2.15 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.004 0.001 PHE A 346 TYR 0.003 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.259 Fit side-chains REVERT: A 294 LYS cc_start: 0.7890 (mttt) cc_final: 0.7584 (tttt) REVERT: B 294 LYS cc_start: 0.7926 (mttt) cc_final: 0.7202 (pttm) REVERT: B 321 LYS cc_start: 0.7867 (mmtt) cc_final: 0.6248 (pttp) REVERT: C 295 ASP cc_start: 0.8062 (p0) cc_final: 0.7739 (p0) REVERT: C 342 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8305 (mt-10) outliers start: 17 outliers final: 17 residues processed: 49 average time/residue: 0.2065 time to fit residues: 11.3584 Evaluate side-chains 54 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.8528 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2169 Z= 0.168 Angle : 0.545 7.622 2904 Z= 0.261 Chirality : 0.050 0.129 330 Planarity : 0.003 0.031 375 Dihedral : 4.207 15.035 291 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.43 % Allowed : 24.90 % Favored : 68.67 % 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: -2.18 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.005 0.002 PHE A 346 TYR 0.005 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.248 Fit side-chains REVERT: A 294 LYS cc_start: 0.7987 (mttt) cc_final: 0.7677 (tttt) REVERT: B 294 LYS cc_start: 0.8060 (mttt) cc_final: 0.7355 (pttm) REVERT: B 321 LYS cc_start: 0.8015 (mmtt) cc_final: 0.6254 (pttp) REVERT: B 351 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: C 295 ASP cc_start: 0.8161 (p0) cc_final: 0.7779 (p0) REVERT: C 342 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8315 (mt-10) outliers start: 16 outliers final: 15 residues processed: 47 average time/residue: 0.1779 time to fit residues: 9.6011 Evaluate side-chains 52 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2169 Z= 0.183 Angle : 0.570 8.345 2904 Z= 0.273 Chirality : 0.050 0.135 330 Planarity : 0.003 0.032 375 Dihedral : 4.379 15.570 291 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 6.02 % Allowed : 25.70 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.006 0.002 PHE A 346 TYR 0.005 0.002 TYR C 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.273 Fit side-chains REVERT: A 294 LYS cc_start: 0.7978 (mttt) cc_final: 0.7655 (tttt) REVERT: B 294 LYS cc_start: 0.8107 (mttt) cc_final: 0.7361 (pttm) REVERT: B 321 LYS cc_start: 0.8035 (mmtt) cc_final: 0.6223 (pttp) REVERT: B 351 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: C 294 LYS cc_start: 0.7730 (mttt) cc_final: 0.7419 (tttt) REVERT: C 342 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8336 (mt-10) outliers start: 15 outliers final: 13 residues processed: 46 average time/residue: 0.2036 time to fit residues: 10.6417 Evaluate side-chains 51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.103511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089592 restraints weight = 3166.445| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.24 r_work: 0.3271 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 2169 Z= 0.291 Angle : 0.675 9.340 2904 Z= 0.329 Chirality : 0.052 0.138 330 Planarity : 0.004 0.033 375 Dihedral : 4.690 16.608 291 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 5.62 % Allowed : 26.51 % Favored : 67.87 % 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: -2.30 (0.44), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 329 PHE 0.006 0.002 PHE A 346 TYR 0.009 0.003 TYR A 310 ARG 0.002 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.30 seconds wall clock time: 23 minutes 28.42 seconds (1408.42 seconds total)