Starting phenix.real_space_refine on Mon Jan 13 13:24:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gg6_51325/01_2025/9gg6_51325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gg6_51325/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gg6_51325/01_2025/9gg6_51325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gg6_51325/01_2025/9gg6_51325.map" model { file = "/net/cci-nas-00/data/ceres_data/9gg6_51325/01_2025/9gg6_51325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gg6_51325/01_2025/9gg6_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-5571/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: 2.58, per 1000 atoms: 1.20 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: 0.46 Conformation dependent library (CDL) restraints added in 380.6 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: 0.50 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: 0.55 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.760 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.350 Find NCS groups from input model: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- 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 : 0.253 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: 0.2702 time to fit residues: 16.5754 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 : 0.274 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.106944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093003 restraints weight = 2935.201| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.24 r_work: 0.3347 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 : 0.257 Fit side-chains REVERT: A 294 LYS cc_start: 0.8058 (mttt) cc_final: 0.7768 (tttt) REVERT: A 351 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: B 294 LYS cc_start: 0.8055 (mttt) cc_final: 0.7375 (pttm) REVERT: B 321 LYS cc_start: 0.7728 (mmtt) cc_final: 0.6136 (pttm) REVERT: B 351 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: C 294 LYS cc_start: 0.8000 (mttt) cc_final: 0.7775 (tttt) REVERT: C 351 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7873 (pt0) outliers start: 18 outliers final: 13 residues processed: 51 average time/residue: 0.2416 time to fit residues: 13.6270 Evaluate side-chains 51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.0770 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.109047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095142 restraints weight = 3049.009| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.28 r_work: 0.3373 rms_B_bonded: 2.41 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: 0.8553 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2169 Z= 0.161 Angle : 0.547 7.093 2904 Z= 0.265 Chirality : 0.050 0.122 330 Planarity : 0.003 0.029 375 Dihedral : 4.100 11.621 291 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 7.23 % Allowed : 23.29 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.45), residues: 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 0.003 0.001 HIS C 329 PHE 0.006 0.002 PHE A 346 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG A 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 57 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.241 Fit side-chains REVERT: A 294 LYS cc_start: 0.8133 (mttt) cc_final: 0.7830 (tttt) REVERT: B 294 LYS cc_start: 0.8062 (mttt) cc_final: 0.7371 (pttm) REVERT: B 321 LYS cc_start: 0.7789 (mmtt) cc_final: 0.6133 (pttp) REVERT: B 349 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8555 (ttm170) REVERT: B 351 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: C 294 LYS cc_start: 0.7930 (mttt) cc_final: 0.7715 (tttt) REVERT: C 351 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7743 (pt0) outliers start: 18 outliers final: 15 residues processed: 52 average time/residue: 0.2440 time to fit residues: 14.0168 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 : 0.253 ------------------------------------------------------------------------------- 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: 8.9990 chunk 7 optimal weight: 0.0040 chunk 10 optimal weight: 0.0030 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.2008 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098358 restraints weight = 2972.150| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.19 r_work: 0.3430 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2023 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= 0.114 Angle : 0.478 6.219 2904 Z= 0.238 Chirality : 0.050 0.123 330 Planarity : 0.003 0.023 375 Dihedral : 3.935 12.609 291 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % 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: -2.39 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (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 0.000 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 58 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.261 Fit side-chains REVERT: A 294 LYS cc_start: 0.8031 (mttt) cc_final: 0.7748 (tttt) REVERT: A 340 LYS cc_start: 0.8516 (mptt) cc_final: 0.8303 (mmtm) REVERT: B 294 LYS cc_start: 0.8003 (mttt) cc_final: 0.7284 (pttm) REVERT: B 321 LYS cc_start: 0.7709 (mmtt) cc_final: 0.6155 (pttm) REVERT: B 349 ARG cc_start: 0.8753 (ttm170) cc_final: 0.8494 (ttm-80) REVERT: B 351 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8183 (pt0) outliers start: 17 outliers final: 15 residues processed: 53 average time/residue: 0.2574 time to fit residues: 15.1075 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 : 0.267 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.108185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094130 restraints weight = 3083.010| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.27 r_work: 0.3359 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2202 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 : 0.539 6.461 2904 Z= 0.266 Chirality : 0.050 0.123 330 Planarity : 0.003 0.030 375 Dihedral : 4.084 14.716 291 Min Nonbonded Distance : 2.561 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 (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: -2.31 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (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 C 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 57 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.252 Fit side-chains REVERT: A 290 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7733 (mttt) REVERT: A 294 LYS cc_start: 0.8082 (mttt) cc_final: 0.7758 (tttt) REVERT: B 294 LYS cc_start: 0.8120 (mttt) cc_final: 0.7441 (pttm) REVERT: B 321 LYS cc_start: 0.7929 (mmtt) cc_final: 0.6250 (pttp) REVERT: B 349 ARG cc_start: 0.8783 (ttm170) cc_final: 0.8383 (ttm170) REVERT: B 351 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: C 351 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7719 (pt0) outliers start: 18 outliers final: 13 residues processed: 52 average time/residue: 0.2720 time to fit residues: 15.7114 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 : 0.395 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 0.0170 chunk 20 optimal weight: 0.0170 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.117959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104191 restraints weight = 2934.800| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.21 r_work: 0.3519 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2247 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= 0.079 Angle : 0.487 7.098 2904 Z= 0.237 Chirality : 0.050 0.123 330 Planarity : 0.002 0.017 375 Dihedral : 3.852 16.520 291 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.82 % Allowed : 27.71 % 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 (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: -2.19 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.003 0.001 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG A 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 56 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.262 Fit side-chains REVERT: A 294 LYS cc_start: 0.7993 (mttt) cc_final: 0.7703 (tttt) REVERT: B 294 LYS cc_start: 0.7975 (mttt) cc_final: 0.7261 (pttm) REVERT: B 321 LYS cc_start: 0.7581 (mmtt) cc_final: 0.6127 (pttm) outliers start: 12 outliers final: 10 residues processed: 53 average time/residue: 0.2497 time to fit residues: 14.6512 Evaluate side-chains 51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS 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 B residue 352 SER Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.0050 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.115100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101075 restraints weight = 3013.397| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.26 r_work: 0.3473 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2169 Z= 0.095 Angle : 0.483 7.276 2904 Z= 0.230 Chirality : 0.050 0.121 330 Planarity : 0.002 0.023 375 Dihedral : 3.805 16.738 291 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.66 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 (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: -2.12 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (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 0.004 0.001 TYR B 310 ARG 0.001 0.000 ARG C 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 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.258 Fit side-chains REVERT: A 294 LYS cc_start: 0.8106 (mttt) cc_final: 0.7835 (tttt) REVERT: B 294 LYS cc_start: 0.8027 (mttt) cc_final: 0.7314 (pttm) REVERT: B 321 LYS cc_start: 0.7653 (mmtt) cc_final: 0.6118 (pttm) outliers start: 15 outliers final: 13 residues processed: 49 average time/residue: 0.2330 time to fit residues: 12.7462 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 : 0.261 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 0.3980 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.105968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092046 restraints weight = 3201.517| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.30 r_work: 0.3329 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2169 Z= 0.203 Angle : 0.561 7.578 2904 Z= 0.275 Chirality : 0.050 0.130 330 Planarity : 0.004 0.036 375 Dihedral : 4.333 18.516 291 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.83 % Allowed : 24.10 % 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 (0.45), 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 0.007 0.002 PHE A 346 TYR 0.007 0.002 TYR C 310 ARG 0.002 0.000 ARG C 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 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.244 Fit side-chains REVERT: A 294 LYS cc_start: 0.8153 (mttt) cc_final: 0.7839 (tttt) REVERT: B 294 LYS cc_start: 0.8225 (mttt) cc_final: 0.7504 (pttm) REVERT: B 321 LYS cc_start: 0.8004 (mmtt) cc_final: 0.6254 (pttp) outliers start: 17 outliers final: 14 residues processed: 47 average time/residue: 0.2217 time to fit residues: 11.6526 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 : 0.261 ------------------------------------------------------------------------------- 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 324 SER 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 322 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.107242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093429 restraints weight = 3160.814| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.25 r_work: 0.3355 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2610 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= 0.179 Angle : 0.559 7.983 2904 Z= 0.269 Chirality : 0.050 0.128 330 Planarity : 0.004 0.034 375 Dihedral : 4.356 18.545 291 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.57 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 (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: -2.23 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 A 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 50 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.262 Fit side-chains REVERT: A 294 LYS cc_start: 0.8173 (mttt) cc_final: 0.7860 (tttt) REVERT: B 294 LYS cc_start: 0.8198 (mttt) cc_final: 0.7480 (pttm) REVERT: B 321 LYS cc_start: 0.8062 (mmtt) cc_final: 0.6299 (pttp) outliers start: 15 outliers final: 13 residues processed: 46 average time/residue: 0.2137 time to fit residues: 11.2414 Evaluate side-chains 49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5140 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.116310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102485 restraints weight = 2991.853| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.28 r_work: 0.3509 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2169 Z= 0.080 Angle : 0.472 7.361 2904 Z= 0.227 Chirality : 0.050 0.121 330 Planarity : 0.002 0.022 375 Dihedral : 3.957 16.825 291 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.42 % Allowed : 26.10 % Favored : 69.48 % 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: -2.12 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.003 0.001 PHE B 346 TYR 0.003 0.001 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 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.258 Fit side-chains REVERT: A 294 LYS cc_start: 0.8039 (mttt) cc_final: 0.7787 (tttt) REVERT: B 294 LYS cc_start: 0.8020 (mttt) cc_final: 0.7299 (pttm) REVERT: B 321 LYS cc_start: 0.7755 (mmtt) cc_final: 0.6182 (pttm) outliers start: 11 outliers final: 11 residues processed: 49 average time/residue: 0.2222 time to fit residues: 12.1720 Evaluate side-chains 50 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 324 SER 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 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 269 GLN 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: 10.0000 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN C 286 ASN C 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.103774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089768 restraints weight = 3124.522| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.24 r_work: 0.3279 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 2169 Z= 0.311 Angle : 0.687 9.552 2904 Z= 0.336 Chirality : 0.052 0.138 330 Planarity : 0.004 0.039 375 Dihedral : 4.681 18.865 291 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 5.62 % Allowed : 26.10 % 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: -2.26 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 329 PHE 0.007 0.003 PHE C 346 TYR 0.010 0.003 TYR A 310 ARG 0.003 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1759.37 seconds wall clock time: 32 minutes 31.70 seconds (1951.70 seconds total)