Starting phenix.real_space_refine on Wed Sep 17 02:58:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gg6_51325/09_2025/9gg6_51325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gg6_51325/09_2025/9gg6_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gg6_51325/09_2025/9gg6_51325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gg6_51325/09_2025/9gg6_51325_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gg6_51325/09_2025/9gg6_51325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gg6_51325/09_2025/9gg6_51325.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C Time building chain proxies: 0.38, per 1000 atoms: 0.18 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: 0.08 Conformation dependent library (CDL) restraints added in 50.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 0.12 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.190 Find NCS groups from input model: 0.010 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.470 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 349 TYR 0.003 0.001 TYR C 310 PHE 0.008 0.003 PHE A 346 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2169) covalent geometry : angle 0.70978 ( 2904) *********************** 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 : 0.048 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: 0.0720 time to fit residues: 4.4349 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 : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.0970 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.108342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094263 restraints weight = 2973.156| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.27 r_work: 0.3368 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2169 Z= 0.197 Angle : 0.591 8.127 2904 Z= 0.287 Chirality : 0.050 0.131 330 Planarity : 0.004 0.038 375 Dihedral : 4.224 9.906 291 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 7.23 % Allowed : 21.69 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.44), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 349 TYR 0.007 0.002 TYR C 310 PHE 0.007 0.002 PHE A 346 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 2169) covalent geometry : angle 0.59114 ( 2904) *********************** 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 54 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.046 Fit side-chains REVERT: A 294 LYS cc_start: 0.8013 (mttt) cc_final: 0.7731 (tttt) REVERT: A 321 LYS cc_start: 0.7393 (mmtt) cc_final: 0.6943 (mmmm) REVERT: B 294 LYS cc_start: 0.8034 (mttt) cc_final: 0.7357 (pttm) REVERT: B 321 LYS cc_start: 0.7635 (mmtt) cc_final: 0.6100 (pttp) REVERT: B 351 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: C 294 LYS cc_start: 0.7956 (mttt) cc_final: 0.7739 (tttt) REVERT: C 351 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7886 (pt0) outliers start: 18 outliers final: 13 residues processed: 50 average time/residue: 0.0671 time to fit residues: 3.6959 Evaluate side-chains 49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095654 restraints weight = 3053.008| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.21 r_work: 0.3390 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2169 Z= 0.152 Angle : 0.528 7.418 2904 Z= 0.256 Chirality : 0.050 0.122 330 Planarity : 0.003 0.030 375 Dihedral : 4.058 11.307 291 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 6.83 % Allowed : 22.89 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.005 0.001 TYR C 310 PHE 0.006 0.002 PHE A 346 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2169) covalent geometry : angle 0.52782 ( 2904) *********************** 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 54 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.099 Fit side-chains REVERT: A 294 LYS cc_start: 0.8080 (mttt) cc_final: 0.7782 (tttt) REVERT: B 294 LYS cc_start: 0.7999 (mttt) cc_final: 0.7302 (pttm) REVERT: B 321 LYS cc_start: 0.7699 (mmtt) cc_final: 0.6098 (pttm) REVERT: B 349 ARG cc_start: 0.8733 (ttm170) cc_final: 0.8377 (ttm170) REVERT: B 351 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: C 294 LYS cc_start: 0.7932 (mttt) cc_final: 0.7706 (tttt) REVERT: C 351 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7778 (pt0) outliers start: 17 outliers final: 15 residues processed: 49 average time/residue: 0.1093 time to fit residues: 5.9360 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 : 0.092 ------------------------------------------------------------------------------- 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 311 LYS Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.110659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096759 restraints weight = 3042.080| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.25 r_work: 0.3403 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2169 Z= 0.130 Angle : 0.483 6.335 2904 Z= 0.241 Chirality : 0.049 0.121 330 Planarity : 0.003 0.026 375 Dihedral : 3.955 12.352 291 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.005 0.001 TYR C 310 PHE 0.005 0.002 PHE A 346 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2169) covalent geometry : angle 0.48314 ( 2904) *********************** 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 59 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.103 Fit side-chains REVERT: A 294 LYS cc_start: 0.8019 (mttt) cc_final: 0.7702 (tttt) REVERT: B 294 LYS cc_start: 0.7984 (mttt) cc_final: 0.7268 (pttm) REVERT: B 321 LYS cc_start: 0.7694 (mmtt) cc_final: 0.6120 (pttm) REVERT: B 351 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: C 351 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7702 (pt0) outliers start: 17 outliers final: 14 residues processed: 54 average time/residue: 0.1138 time to fit residues: 6.7483 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 : 0.090 ------------------------------------------------------------------------------- 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 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 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 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 20 optimal weight: 0.1980 overall best weight: 1.2522 ------------------------------------------------------------------------------- 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098084 restraints weight = 3063.119| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.22 r_work: 0.3424 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2126 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= 0.118 Angle : 0.513 6.357 2904 Z= 0.252 Chirality : 0.050 0.122 330 Planarity : 0.003 0.023 375 Dihedral : 3.873 13.259 291 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 7.23 % Allowed : 24.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 349 TYR 0.004 0.001 TYR C 310 PHE 0.005 0.002 PHE A 346 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2169) covalent geometry : angle 0.51278 ( 2904) *********************** 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 60 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.098 Fit side-chains REVERT: A 294 LYS cc_start: 0.8059 (mttt) cc_final: 0.7770 (tttt) REVERT: A 340 LYS cc_start: 0.8532 (mptt) cc_final: 0.8286 (mmtm) REVERT: B 294 LYS cc_start: 0.8018 (mttt) cc_final: 0.7324 (pttm) REVERT: B 321 LYS cc_start: 0.7712 (mmtt) cc_final: 0.6125 (pttm) outliers start: 18 outliers final: 14 residues processed: 55 average time/residue: 0.1115 time to fit residues: 6.7390 Evaluate side-chains 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101040 restraints weight = 2965.558| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.25 r_work: 0.3469 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2169 Z= 0.095 Angle : 0.490 6.536 2904 Z= 0.242 Chirality : 0.050 0.121 330 Planarity : 0.002 0.019 375 Dihedral : 3.897 16.201 291 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.02 % Allowed : 25.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 349 TYR 0.003 0.001 TYR C 310 PHE 0.004 0.001 PHE A 346 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 2169) covalent geometry : angle 0.48978 ( 2904) *********************** 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 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.093 Fit side-chains REVERT: A 294 LYS cc_start: 0.7980 (mttt) cc_final: 0.7692 (tttt) REVERT: B 294 LYS cc_start: 0.8014 (mttt) cc_final: 0.7303 (pttm) REVERT: B 321 LYS cc_start: 0.7654 (mmtt) cc_final: 0.6113 (pttp) outliers start: 15 outliers final: 14 residues processed: 48 average time/residue: 0.1059 time to fit residues: 5.6285 Evaluate side-chains 50 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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 311 LYS Chi-restraints excluded: chain B residue 325 LEU 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 17 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094363 restraints weight = 3042.463| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.28 r_work: 0.3368 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2316 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= 0.161 Angle : 0.563 7.486 2904 Z= 0.272 Chirality : 0.050 0.123 330 Planarity : 0.003 0.028 375 Dihedral : 4.166 17.418 291 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.02 % Allowed : 26.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG C 349 TYR 0.006 0.002 TYR C 310 PHE 0.006 0.002 PHE A 346 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2169) covalent geometry : angle 0.56274 ( 2904) *********************** 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 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.090 Fit side-chains REVERT: A 294 LYS cc_start: 0.8117 (mttt) cc_final: 0.7824 (tttt) REVERT: B 294 LYS cc_start: 0.8163 (mttt) cc_final: 0.7494 (pttm) REVERT: B 321 LYS cc_start: 0.7863 (mmtt) cc_final: 0.6201 (pttp) REVERT: C 351 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7610 (pt0) outliers start: 15 outliers final: 13 residues processed: 48 average time/residue: 0.1040 time to fit residues: 5.5659 Evaluate side-chains 52 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.0770 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.1918 ------------------------------------------------------------------------------- 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 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.097797 restraints weight = 3096.785| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.26 r_work: 0.3411 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2169 Z= 0.112 Angle : 0.525 7.397 2904 Z= 0.250 Chirality : 0.050 0.127 330 Planarity : 0.003 0.022 375 Dihedral : 4.077 17.287 291 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 6.02 % Allowed : 26.51 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.004 0.001 TYR B 310 PHE 0.004 0.001 PHE A 346 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2169) covalent geometry : angle 0.52532 ( 2904) *********************** 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 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.103 Fit side-chains REVERT: A 294 LYS cc_start: 0.8032 (mttt) cc_final: 0.7752 (tttt) REVERT: B 294 LYS cc_start: 0.8096 (mttt) cc_final: 0.7410 (pttm) REVERT: B 321 LYS cc_start: 0.7788 (mmtt) cc_final: 0.6169 (pttm) outliers start: 15 outliers final: 14 residues processed: 48 average time/residue: 0.1017 time to fit residues: 5.4221 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 : 0.090 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.107280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093490 restraints weight = 3080.323| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.26 r_work: 0.3352 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2169 Z= 0.163 Angle : 0.546 7.142 2904 Z= 0.266 Chirality : 0.050 0.126 330 Planarity : 0.003 0.031 375 Dihedral : 4.266 18.431 291 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.02 % Allowed : 26.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG C 349 TYR 0.006 0.002 TYR C 310 PHE 0.005 0.002 PHE A 346 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2169) covalent geometry : angle 0.54645 ( 2904) *********************** 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: 15 poor density : 37 time to evaluate : 0.094 Fit side-chains REVERT: A 294 LYS cc_start: 0.8122 (mttt) cc_final: 0.7819 (tttt) REVERT: B 294 LYS cc_start: 0.8176 (mttt) cc_final: 0.7444 (pttm) REVERT: B 321 LYS cc_start: 0.7977 (mmtt) cc_final: 0.6263 (pttp) outliers start: 15 outliers final: 14 residues processed: 47 average time/residue: 0.1061 time to fit residues: 5.5365 Evaluate side-chains 49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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 C residue 269 GLN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 317 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: 10.0000 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.0870 chunk 20 optimal weight: 0.1980 chunk 8 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.6580 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.108601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094710 restraints weight = 3108.735| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.28 r_work: 0.3371 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2169 Z= 0.140 Angle : 0.570 8.043 2904 Z= 0.274 Chirality : 0.050 0.131 330 Planarity : 0.003 0.031 375 Dihedral : 4.279 18.256 291 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 349 TYR 0.004 0.001 TYR C 310 PHE 0.005 0.002 PHE A 346 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2169) covalent geometry : angle 0.57007 ( 2904) ********************** 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 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.088 Fit side-chains REVERT: A 294 LYS cc_start: 0.8116 (mttt) cc_final: 0.7815 (tttt) REVERT: B 294 LYS cc_start: 0.8181 (mttt) cc_final: 0.7449 (pttm) REVERT: B 321 LYS cc_start: 0.7962 (mmtt) cc_final: 0.6265 (pttp) outliers start: 14 outliers final: 13 residues processed: 48 average time/residue: 0.1231 time to fit residues: 6.5259 Evaluate side-chains 51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.105692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091916 restraints weight = 3127.632| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.25 r_work: 0.3325 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2169 Z= 0.202 Angle : 0.606 8.223 2904 Z= 0.293 Chirality : 0.050 0.127 330 Planarity : 0.004 0.035 375 Dihedral : 4.473 18.549 291 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 : 6.02 % Allowed : 26.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.006 0.002 TYR C 310 PHE 0.006 0.002 PHE A 346 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 2169) covalent geometry : angle 0.60638 ( 2904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 876.13 seconds wall clock time: 15 minutes 55.67 seconds (955.67 seconds total)