Starting phenix.real_space_refine on Wed Mar 5 21:23:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ore_17121/03_2025/8ore_17121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ore_17121/03_2025/8ore_17121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ore_17121/03_2025/8ore_17121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ore_17121/03_2025/8ore_17121.map" model { file = "/net/cci-nas-00/data/ceres_data/8ore_17121/03_2025/8ore_17121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ore_17121/03_2025/8ore_17121.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 1110 2.51 5 N 327 2.21 5 O 330 1.98 5 H 1845 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3615 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 2.49, per 1000 atoms: 0.69 Number of scatterers: 3615 At special positions: 0 Unit cell: (82.84, 81.75, 37.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 330 8.00 N 327 7.00 C 1110 6.00 H 1845 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.85 Conformation dependent library (CDL) restraints added in 244.7 milliseconds 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 402 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.612A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 361 removed outlier: 6.938A pdb=" N SER B 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY A 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER C 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 62 hydrogen bonds defined for protein. 186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 1842 1.11 - 1.29: 297 1.29 - 1.46: 490 1.46 - 1.63: 1010 1.63 - 1.81: 3 Bond restraints: 3642 Sorted by residual: bond pdb=" N GLY A 366 " pdb=" H GLY A 366 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 HIS A 362 " pdb=" HE1 HIS A 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 HIS B 362 " pdb=" HE1 HIS B 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU C 315 " pdb=" H LEU C 315 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 315 " pdb=" H LEU B 315 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 3637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 5360 2.37 - 4.75: 912 4.75 - 7.12: 334 7.12 - 9.50: 32 9.50 - 11.87: 4 Bond angle restraints: 6642 Sorted by residual: angle pdb=" C LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta sigma weight residual 111.14 119.05 -7.91 1.39e+00 5.18e-01 3.24e+01 angle pdb=" C LEU B 325 " pdb=" CA LEU B 325 " pdb=" CB LEU B 325 " ideal model delta sigma weight residual 111.40 118.42 -7.02 1.29e+00 6.01e-01 2.96e+01 angle pdb=" N PRO B 364 " pdb=" CA PRO B 364 " pdb=" C PRO B 364 " ideal model delta sigma weight residual 113.57 120.57 -7.00 1.31e+00 5.83e-01 2.86e+01 angle pdb=" CB HIS B 362 " pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 131.20 124.91 6.29 1.30e+00 5.92e-01 2.34e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 118.61 -4.81 1.00e+00 1.00e+00 2.31e+01 ... (remaining 6637 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.53: 1439 13.53 - 27.06: 117 27.06 - 40.59: 35 40.59 - 54.12: 28 54.12 - 67.65: 52 Dihedral angle restraints: 1671 sinusoidal: 960 harmonic: 711 Sorted by residual: dihedral pdb=" C LEU A 325 " pdb=" N LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta harmonic sigma weight residual -122.60 -138.99 16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C VAL B 363 " pdb=" N VAL B 363 " pdb=" CA VAL B 363 " pdb=" CB VAL B 363 " ideal model delta harmonic sigma weight residual -122.00 -137.70 15.70 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -136.54 14.54 0 2.50e+00 1.60e-01 3.38e+01 ... (remaining 1668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 200 0.120 - 0.240: 40 0.240 - 0.360: 16 0.360 - 0.479: 9 0.479 - 0.599: 2 Chirality restraints: 267 Sorted by residual: chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CA PRO B 364 " pdb=" N PRO B 364 " pdb=" C PRO B 364 " pdb=" CB PRO B 364 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA VAL B 363 " pdb=" N VAL B 363 " pdb=" C VAL B 363 " pdb=" CB VAL B 363 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 264 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.099 2.00e-02 2.50e+03 4.00e-02 4.80e+01 pdb=" CG PHE A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 346 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 346 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 346 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 346 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 346 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " 0.076 2.00e-02 2.50e+03 3.28e-02 3.23e+01 pdb=" CG PHE B 346 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " 0.012 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 341 " -0.030 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" N GLU B 342 " 0.095 2.00e-02 2.50e+03 pdb=" CA GLU B 342 " -0.027 2.00e-02 2.50e+03 pdb=" H GLU B 342 " -0.038 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 317 2.21 - 2.81: 6754 2.81 - 3.40: 9317 3.40 - 4.00: 12465 4.00 - 4.60: 17899 Nonbonded interactions: 46752 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.611 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.636 2.450 nonbonded pdb=" HG1 THR A 377 " pdb=" OE1 GLU A 380 " model vdw 1.650 2.450 nonbonded pdb=" HG1 THR C 377 " pdb=" OE2 GLU C 380 " model vdw 1.662 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.675 2.450 ... (remaining 46747 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: 0.01 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: 0.780 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: 0.060 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.080 Find NCS groups from input model: 0.080 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:20.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 : 0.011 0.052 1797 Z= 0.718 Angle : 2.085 10.566 2400 Z= 1.353 Chirality : 0.140 0.599 267 Planarity : 0.011 0.065 306 Dihedral : 10.934 54.560 696 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Cbeta Deviations : 3.48 % 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: -2.10 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 362 PHE 0.055 0.024 PHE B 378 TYR 0.040 0.012 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8330 (t0) cc_final: 0.8073 (t0) REVERT: A 349 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7794 (ttp-110) REVERT: B 314 ASP cc_start: 0.8198 (t0) cc_final: 0.7914 (t0) REVERT: B 317 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7384 (ptpp) REVERT: B 347 LYS cc_start: 0.8635 (mttt) cc_final: 0.8389 (mttp) REVERT: C 307 GLN cc_start: 0.7873 (tt0) cc_final: 0.7448 (tt0) REVERT: C 338 GLU cc_start: 0.8150 (tt0) cc_final: 0.7887 (tt0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 2.5516 time to fit residues: 212.2105 Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 368 ASN A 374 HIS B 307 GLN B 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.149230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.129026 restraints weight = 5990.990| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.98 r_work: 0.3937 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1797 Z= 0.181 Angle : 0.697 4.506 2400 Z= 0.358 Chirality : 0.055 0.151 267 Planarity : 0.004 0.036 306 Dihedral : 7.165 22.681 237 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.98 % Allowed : 20.40 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.002 PHE A 378 TYR 0.006 0.002 TYR B 310 ARG 0.007 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8128 (t0) cc_final: 0.7808 (t0) REVERT: A 372 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: B 314 ASP cc_start: 0.8591 (t0) cc_final: 0.8372 (t0) REVERT: B 317 LYS cc_start: 0.8374 (ptmt) cc_final: 0.8060 (ptpp) REVERT: B 319 THR cc_start: 0.8571 (m) cc_final: 0.8221 (p) REVERT: B 347 LYS cc_start: 0.8040 (mttt) cc_final: 0.7760 (mttp) outliers start: 10 outliers final: 3 residues processed: 65 average time/residue: 2.3971 time to fit residues: 158.3499 Evaluate side-chains 49 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 0.0050 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.148647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.129618 restraints weight = 6103.509| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.97 r_work: 0.3924 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1797 Z= 0.141 Angle : 0.610 4.657 2400 Z= 0.307 Chirality : 0.053 0.136 267 Planarity : 0.003 0.035 306 Dihedral : 6.080 17.855 237 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.48 % Allowed : 24.38 % Favored : 72.14 % 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: -2.14 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.010 0.002 PHE A 378 TYR 0.006 0.001 TYR C 310 ARG 0.007 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8084 (t0) cc_final: 0.7784 (t0) REVERT: A 359 ASN cc_start: 0.8992 (m-40) cc_final: 0.8766 (m-40) REVERT: B 319 THR cc_start: 0.8557 (m) cc_final: 0.8229 (p) REVERT: B 345 ASP cc_start: 0.7608 (t0) cc_final: 0.7186 (t70) REVERT: C 274 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7778 (ttpp) REVERT: C 336 GLN cc_start: 0.8432 (tt0) cc_final: 0.8123 (mt0) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 2.0710 time to fit residues: 113.9694 Evaluate side-chains 53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.146036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.126224 restraints weight = 6175.455| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.04 r_work: 0.3893 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1797 Z= 0.171 Angle : 0.605 4.672 2400 Z= 0.303 Chirality : 0.052 0.142 267 Planarity : 0.004 0.037 306 Dihedral : 5.898 19.325 237 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.99 % Allowed : 23.88 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.46), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.011 0.002 PHE A 378 TYR 0.005 0.001 TYR C 310 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8116 (t0) cc_final: 0.7851 (t0) REVERT: A 359 ASN cc_start: 0.9031 (m-40) cc_final: 0.8817 (m-40) REVERT: B 319 THR cc_start: 0.8591 (m) cc_final: 0.8270 (p) REVERT: B 345 ASP cc_start: 0.7671 (t0) cc_final: 0.7225 (t70) REVERT: C 336 GLN cc_start: 0.8546 (tt0) cc_final: 0.8278 (mt0) REVERT: C 380 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6575 (mt-10) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 1.9936 time to fit residues: 109.8460 Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.140293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120495 restraints weight = 6317.697| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.08 r_work: 0.3808 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1797 Z= 0.234 Angle : 0.628 4.901 2400 Z= 0.319 Chirality : 0.053 0.156 267 Planarity : 0.004 0.044 306 Dihedral : 6.021 21.108 237 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.47 % Allowed : 22.89 % Favored : 71.64 % 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: -2.09 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.015 0.002 PHE A 378 TYR 0.006 0.001 TYR C 310 ARG 0.005 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8123 (t0) cc_final: 0.7839 (t0) REVERT: A 349 ARG cc_start: 0.7719 (ttp-110) cc_final: 0.7508 (ttp-110) REVERT: B 319 THR cc_start: 0.8533 (m) cc_final: 0.8199 (p) REVERT: B 345 ASP cc_start: 0.7648 (t0) cc_final: 0.7101 (t70) REVERT: C 274 LYS cc_start: 0.7958 (ttpp) cc_final: 0.7555 (tttm) REVERT: C 336 GLN cc_start: 0.8566 (tt0) cc_final: 0.8289 (mt0) REVERT: C 345 ASP cc_start: 0.7888 (t0) cc_final: 0.7365 (t70) REVERT: C 349 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7077 (mtp180) outliers start: 11 outliers final: 4 residues processed: 53 average time/residue: 2.0736 time to fit residues: 111.9249 Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.137954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.117316 restraints weight = 6300.041| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.07 r_work: 0.3784 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1797 Z= 0.275 Angle : 0.657 5.175 2400 Z= 0.334 Chirality : 0.053 0.159 267 Planarity : 0.005 0.047 306 Dihedral : 6.161 23.041 237 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.48 % Allowed : 24.38 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.015 0.002 PHE A 378 TYR 0.006 0.001 TYR C 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8356 (tttp) REVERT: A 345 ASP cc_start: 0.8119 (t0) cc_final: 0.7832 (t0) REVERT: B 319 THR cc_start: 0.8576 (m) cc_final: 0.8233 (p) REVERT: B 345 ASP cc_start: 0.7668 (t0) cc_final: 0.7130 (t70) REVERT: C 336 GLN cc_start: 0.8569 (tt0) cc_final: 0.8286 (mt0) REVERT: C 345 ASP cc_start: 0.7928 (t0) cc_final: 0.7403 (t70) REVERT: C 349 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7186 (mtp180) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 2.0220 time to fit residues: 107.1767 Evaluate side-chains 54 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.140738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.120941 restraints weight = 6209.442| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.07 r_work: 0.3818 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1797 Z= 0.229 Angle : 0.630 4.788 2400 Z= 0.316 Chirality : 0.052 0.144 267 Planarity : 0.004 0.043 306 Dihedral : 5.837 21.598 237 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.99 % Allowed : 24.88 % Favored : 72.14 % 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 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.009 0.002 PHE C 378 TYR 0.005 0.001 TYR C 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8333 (tttp) REVERT: A 345 ASP cc_start: 0.8083 (t0) cc_final: 0.7820 (t0) REVERT: A 380 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6695 (mt-10) REVERT: B 315 LEU cc_start: 0.9070 (mp) cc_final: 0.8856 (mm) REVERT: B 319 THR cc_start: 0.8669 (m) cc_final: 0.8365 (p) REVERT: B 345 ASP cc_start: 0.7674 (t0) cc_final: 0.7118 (t70) REVERT: C 336 GLN cc_start: 0.8554 (tt0) cc_final: 0.8269 (mt0) REVERT: C 345 ASP cc_start: 0.7917 (t0) cc_final: 0.7420 (t70) REVERT: C 349 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7156 (mtp180) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 2.0884 time to fit residues: 106.4437 Evaluate side-chains 53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.146598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.127252 restraints weight = 6128.742| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.07 r_work: 0.3900 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1797 Z= 0.162 Angle : 0.578 3.896 2400 Z= 0.286 Chirality : 0.051 0.124 267 Planarity : 0.004 0.035 306 Dihedral : 5.314 18.328 237 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.48 % Allowed : 24.38 % Favored : 72.14 % 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 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8327 (tttp) REVERT: A 380 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6663 (mt-10) REVERT: B 315 LEU cc_start: 0.9080 (mp) cc_final: 0.8873 (mm) REVERT: B 319 THR cc_start: 0.8570 (m) cc_final: 0.8282 (p) REVERT: B 345 ASP cc_start: 0.7625 (t0) cc_final: 0.7047 (t70) REVERT: C 336 GLN cc_start: 0.8538 (tt0) cc_final: 0.8263 (mt0) REVERT: C 345 ASP cc_start: 0.7895 (t0) cc_final: 0.7431 (t70) REVERT: C 349 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7077 (mtp180) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 2.1026 time to fit residues: 105.0021 Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.144437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.124437 restraints weight = 6090.576| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.03 r_work: 0.3881 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 1797 Z= 0.163 Angle : 0.578 4.233 2400 Z= 0.286 Chirality : 0.051 0.127 267 Planarity : 0.003 0.035 306 Dihedral : 5.167 16.313 237 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.49 % Allowed : 25.87 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.001 PHE B 378 TYR 0.004 0.001 TYR C 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8314 (tttp) REVERT: B 315 LEU cc_start: 0.9055 (mp) cc_final: 0.8848 (mm) REVERT: B 319 THR cc_start: 0.8569 (m) cc_final: 0.8284 (p) REVERT: B 345 ASP cc_start: 0.7617 (t0) cc_final: 0.7013 (t70) REVERT: C 336 GLN cc_start: 0.8534 (tt0) cc_final: 0.8266 (mt0) REVERT: C 345 ASP cc_start: 0.7906 (t0) cc_final: 0.7394 (t70) REVERT: C 349 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7118 (mtp85) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 2.2032 time to fit residues: 114.5334 Evaluate side-chains 51 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.149813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.131121 restraints weight = 6309.695| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.07 r_work: 0.3975 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 1797 Z= 0.173 Angle : 0.585 4.646 2400 Z= 0.291 Chirality : 0.051 0.124 267 Planarity : 0.004 0.033 306 Dihedral : 5.115 17.411 237 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.49 % Allowed : 27.36 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.003 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8329 (tttp) REVERT: B 315 LEU cc_start: 0.9032 (mp) cc_final: 0.8808 (mm) REVERT: B 319 THR cc_start: 0.8585 (m) cc_final: 0.8297 (p) REVERT: B 345 ASP cc_start: 0.7525 (t0) cc_final: 0.7011 (t70) REVERT: C 336 GLN cc_start: 0.8568 (tt0) cc_final: 0.8330 (mt0) REVERT: C 345 ASP cc_start: 0.7827 (t0) cc_final: 0.7365 (t70) REVERT: C 349 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7105 (mtp85) outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 2.1930 time to fit residues: 111.7510 Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.153860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.134207 restraints weight = 6192.394| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.13 r_work: 0.4002 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 1797 Z= 0.170 Angle : 0.576 4.565 2400 Z= 0.285 Chirality : 0.051 0.123 267 Planarity : 0.003 0.032 306 Dihedral : 4.917 14.754 237 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.49 % Allowed : 27.36 % Favored : 71.14 % 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: -2.09 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.005 0.001 PHE B 378 TYR 0.004 0.001 TYR C 310 ARG 0.003 0.001 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4417.90 seconds wall clock time: 75 minutes 36.61 seconds (4536.61 seconds total)