Starting phenix.real_space_refine on Mon Feb 10 22:16:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e3c_30979/02_2025/7e3c_30979.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e3c_30979/02_2025/7e3c_30979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e3c_30979/02_2025/7e3c_30979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e3c_30979/02_2025/7e3c_30979.map" model { file = "/net/cci-nas-00/data/ceres_data/7e3c_30979/02_2025/7e3c_30979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e3c_30979/02_2025/7e3c_30979.cif" } resolution = 4.2 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 15 5.16 5 C 1865 2.51 5 N 493 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2937 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "C" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 655 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 3, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 732 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 2, 'TRANS': 106} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.85, per 1000 atoms: 0.97 Number of scatterers: 2937 At special positions: 0 Unit cell: (64.133, 56.524, 95.656, 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 15 16.00 O 564 8.00 N 493 7.00 C 1865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 374.4 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.9% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.962A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.880A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.456A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'C' and resid 57 through 61 removed outlier: 4.282A pdb=" N ARG C 61 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.206A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.173A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 removed outlier: 3.613A pdb=" N TYR B 79 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 59 removed outlier: 4.167A pdb=" N TYR B 33 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 96 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B 97 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 92 hydrogen bonds defined for protein. 222 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: 0.71 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.52: 2204 1.52 - 1.81: 801 1.81 - 2.11: 2 2.11 - 2.40: 0 2.40 - 2.69: 1 Bond restraints: 3008 Sorted by residual: bond pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 1.332 2.695 -1.362 1.40e-02 5.10e+03 9.47e+03 bond pdb=" CA ILE B 69 " pdb=" CB ILE B 69 " ideal model delta sigma weight residual 1.551 1.530 0.020 1.08e-02 8.57e+03 3.50e+00 bond pdb=" N ARG B 71 " pdb=" CA ARG B 71 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.49e+00 bond pdb=" N HIS B 72 " pdb=" CA HIS B 72 " ideal model delta sigma weight residual 1.461 1.483 -0.022 1.20e-02 6.94e+03 3.22e+00 bond pdb=" C PRO C 95 " pdb=" N PRO C 96 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.74e+00 ... (remaining 3003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.57: 4107 10.57 - 21.14: 1 21.14 - 31.71: 0 31.71 - 42.28: 1 42.28 - 52.85: 2 Bond angle restraints: 4111 Sorted by residual: angle pdb=" O HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 123.26 70.41 52.85 1.24e+00 6.50e-01 1.82e+03 angle pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 116.71 66.92 49.79 1.30e+00 5.92e-01 1.47e+03 angle pdb=" C HIS B 72 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 121.54 156.28 -34.74 1.91e+00 2.74e-01 3.31e+02 angle pdb=" N PRO C 59 " pdb=" CA PRO C 59 " pdb=" CB PRO C 59 " ideal model delta sigma weight residual 103.20 110.16 -6.96 9.50e-01 1.11e+00 5.37e+01 angle pdb=" N PRO B 14 " pdb=" CA PRO B 14 " pdb=" CB PRO B 14 " ideal model delta sigma weight residual 103.25 110.58 -7.33 1.05e+00 9.07e-01 4.87e+01 ... (remaining 4106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 1559 17.30 - 34.61: 154 34.61 - 51.91: 21 51.91 - 69.21: 7 69.21 - 86.51: 2 Dihedral angle restraints: 1743 sinusoidal: 581 harmonic: 1162 Sorted by residual: dihedral pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta harmonic sigma weight residual -180.00 -117.44 -62.56 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.09 55.91 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 148.00 -55.00 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 1740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 331 0.052 - 0.104: 97 0.104 - 0.156: 18 0.156 - 0.208: 3 0.208 - 0.260: 3 Chirality restraints: 452 Sorted by residual: chirality pdb=" CA PRO C 59 " pdb=" N PRO C 59 " pdb=" C PRO C 59 " pdb=" CB PRO C 59 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO C 8 " pdb=" N PRO C 8 " pdb=" C PRO C 8 " pdb=" CB PRO C 8 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 449 not shown) Planarity restraints: 541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 72 " 0.184 2.00e-02 2.50e+03 2.33e-01 5.43e+02 pdb=" C HIS B 72 " -0.351 2.00e-02 2.50e+03 pdb=" O HIS B 72 " 0.235 2.00e-02 2.50e+03 pdb=" N ASN B 76 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " 0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 95 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " -0.019 2.00e-02 2.50e+03 1.44e-02 5.15e+00 pdb=" CG TRP B 36 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " -0.002 2.00e-02 2.50e+03 ... (remaining 538 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 136 2.70 - 3.25: 3043 3.25 - 3.80: 4610 3.80 - 4.35: 5626 4.35 - 4.90: 9487 Nonbonded interactions: 22902 Sorted by model distance: nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.151 3.120 nonbonded pdb=" O LEU B 99 " pdb=" N TYR B 102 " model vdw 2.203 3.120 nonbonded pdb=" NZ LYS A 417 " pdb=" OD2 ASP B 100 " model vdw 2.233 3.120 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 33 " model vdw 2.253 3.040 nonbonded pdb=" O ASP C 17 " pdb=" N LEU C 78 " model vdw 2.272 3.120 ... (remaining 22897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.026 1.362 3008 Z= 0.913 Angle : 1.552 52.846 4111 Z= 1.075 Chirality : 0.053 0.260 452 Planarity : 0.012 0.233 540 Dihedral : 13.929 86.511 996 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.22 % Favored : 82.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.63 (0.39), residues: 395 helix: -3.32 (0.69), residues: 34 sheet: -1.46 (0.48), residues: 119 loop : -2.92 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.002 PHE A 342 TYR 0.022 0.002 TYR A 453 ARG 0.005 0.001 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7756 (mtmm) REVERT: A 405 ASP cc_start: 0.8591 (m-30) cc_final: 0.8280 (m-30) REVERT: A 406 GLU cc_start: 0.8704 (pt0) cc_final: 0.8420 (pt0) REVERT: A 474 GLN cc_start: 0.6423 (tp-100) cc_final: 0.6205 (tp-100) REVERT: B 45 LEU cc_start: 0.8621 (mt) cc_final: 0.8137 (mt) REVERT: B 104 MET cc_start: 0.7456 (mtp) cc_final: 0.7089 (mtm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1775 time to fit residues: 9.6032 Evaluate side-chains 41 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.061267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.051661 restraints weight = 12222.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.053454 restraints weight = 7343.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.054758 restraints weight = 4980.240| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3008 Z= 0.223 Angle : 0.710 9.909 4111 Z= 0.371 Chirality : 0.047 0.167 452 Planarity : 0.005 0.056 540 Dihedral : 6.514 44.711 463 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.39), residues: 397 helix: -3.39 (0.70), residues: 34 sheet: -1.26 (0.49), residues: 115 loop : -2.67 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.008 0.001 PHE A 342 TYR 0.016 0.001 TYR B 33 ARG 0.004 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.324 Fit side-chains REVERT: A 405 ASP cc_start: 0.8651 (m-30) cc_final: 0.8355 (m-30) REVERT: A 474 GLN cc_start: 0.6842 (tp-100) cc_final: 0.6483 (tp-100) REVERT: C 31 ASN cc_start: 0.9046 (m-40) cc_final: 0.8817 (m-40) REVERT: C 49 TYR cc_start: 0.6256 (m-10) cc_final: 0.5941 (m-10) REVERT: B 27 LEU cc_start: 0.6281 (tp) cc_final: 0.6029 (tp) REVERT: B 45 LEU cc_start: 0.8604 (mt) cc_final: 0.8180 (mt) REVERT: B 46 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7949 (mm-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1602 time to fit residues: 10.6016 Evaluate side-chains 46 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3048 r_free = 0.3048 target = 0.060553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.050317 restraints weight = 11732.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.052136 restraints weight = 7019.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.053469 restraints weight = 4787.077| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3008 Z= 0.298 Angle : 0.727 10.409 4111 Z= 0.384 Chirality : 0.048 0.162 452 Planarity : 0.006 0.084 540 Dihedral : 6.191 30.658 463 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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: -3.29 (0.39), residues: 397 helix: -3.19 (0.78), residues: 34 sheet: -1.27 (0.49), residues: 114 loop : -2.62 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 107 HIS 0.002 0.001 HIS A 519 PHE 0.010 0.001 PHE A 342 TYR 0.021 0.002 TYR A 489 ARG 0.003 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8663 (m-30) cc_final: 0.8288 (m-30) REVERT: A 406 GLU cc_start: 0.9102 (pt0) cc_final: 0.8892 (pt0) REVERT: A 474 GLN cc_start: 0.6928 (tp-100) cc_final: 0.6569 (tp-100) REVERT: B 27 LEU cc_start: 0.6336 (tp) cc_final: 0.5838 (tp) REVERT: B 45 LEU cc_start: 0.8715 (mt) cc_final: 0.8249 (mt) REVERT: B 46 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7947 (mm-30) REVERT: B 98 ASP cc_start: 0.7522 (m-30) cc_final: 0.7314 (m-30) REVERT: B 104 MET cc_start: 0.7595 (mtt) cc_final: 0.7363 (mtp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1725 time to fit residues: 11.2473 Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.061610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.051826 restraints weight = 11801.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.053589 restraints weight = 7071.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054972 restraints weight = 4838.950| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3008 Z= 0.205 Angle : 0.681 9.192 4111 Z= 0.355 Chirality : 0.045 0.140 452 Planarity : 0.005 0.070 540 Dihedral : 5.580 22.817 463 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -3.04 (0.40), residues: 397 helix: -3.26 (0.75), residues: 34 sheet: -1.13 (0.48), residues: 118 loop : -2.40 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 107 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE A 347 TYR 0.014 0.001 TYR B 33 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.373 Fit side-chains REVERT: A 386 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7564 (mtmm) REVERT: A 405 ASP cc_start: 0.8611 (m-30) cc_final: 0.8215 (m-30) REVERT: A 406 GLU cc_start: 0.9005 (pt0) cc_final: 0.8671 (pt0) REVERT: A 474 GLN cc_start: 0.6778 (tp-100) cc_final: 0.6503 (tp-100) REVERT: C 31 ASN cc_start: 0.8978 (m-40) cc_final: 0.8761 (m-40) REVERT: B 27 LEU cc_start: 0.6148 (tp) cc_final: 0.5785 (tp) REVERT: B 45 LEU cc_start: 0.8540 (mt) cc_final: 0.8077 (mt) REVERT: B 98 ASP cc_start: 0.7640 (m-30) cc_final: 0.6845 (m-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2000 time to fit residues: 12.5860 Evaluate side-chains 46 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.3085 r_free = 0.3085 target = 0.061279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.051348 restraints weight = 11679.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.053178 restraints weight = 6894.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054624 restraints weight = 4656.037| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3008 Z= 0.236 Angle : 0.710 9.560 4111 Z= 0.372 Chirality : 0.047 0.174 452 Planarity : 0.005 0.057 540 Dihedral : 5.592 25.411 463 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -3.01 (0.40), residues: 397 helix: -3.10 (0.79), residues: 34 sheet: -1.18 (0.47), residues: 117 loop : -2.35 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 107 HIS 0.002 0.001 HIS A 519 PHE 0.009 0.001 PHE A 377 TYR 0.013 0.001 TYR B 101 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7510 (mtmm) REVERT: A 405 ASP cc_start: 0.8683 (m-30) cc_final: 0.8296 (m-30) REVERT: A 406 GLU cc_start: 0.9077 (pt0) cc_final: 0.8784 (pt0) REVERT: A 474 GLN cc_start: 0.6904 (tp-100) cc_final: 0.6594 (tp-100) REVERT: B 27 LEU cc_start: 0.6180 (tp) cc_final: 0.5757 (tp) REVERT: B 45 LEU cc_start: 0.8609 (mt) cc_final: 0.8132 (mt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1537 time to fit residues: 10.3580 Evaluate side-chains 44 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.051236 restraints weight = 12059.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.053091 restraints weight = 7053.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.054475 restraints weight = 4729.816| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3008 Z= 0.240 Angle : 0.696 9.578 4111 Z= 0.361 Chirality : 0.046 0.146 452 Planarity : 0.005 0.060 540 Dihedral : 5.482 22.557 463 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -2.95 (0.40), residues: 397 helix: -3.10 (0.76), residues: 34 sheet: -1.23 (0.47), residues: 118 loop : -2.25 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE A 377 TYR 0.013 0.001 TYR B 33 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8041 (mtmm) REVERT: A 405 ASP cc_start: 0.8730 (m-30) cc_final: 0.8339 (m-30) REVERT: A 406 GLU cc_start: 0.8971 (pt0) cc_final: 0.8687 (pt0) REVERT: A 474 GLN cc_start: 0.6872 (tp-100) cc_final: 0.6611 (tp-100) REVERT: B 27 LEU cc_start: 0.6327 (tp) cc_final: 0.5902 (tp) REVERT: B 46 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 98 ASP cc_start: 0.7811 (m-30) cc_final: 0.7010 (m-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1524 time to fit residues: 9.7187 Evaluate side-chains 43 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3075 r_free = 0.3075 target = 0.061285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.051268 restraints weight = 12065.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.053069 restraints weight = 7261.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054095 restraints weight = 4960.315| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3008 Z= 0.232 Angle : 0.698 9.557 4111 Z= 0.363 Chirality : 0.046 0.151 452 Planarity : 0.005 0.051 540 Dihedral : 5.510 24.819 463 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -2.91 (0.40), residues: 397 helix: -3.08 (0.76), residues: 34 sheet: -1.25 (0.47), residues: 118 loop : -2.19 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.010 0.001 PHE A 377 TYR 0.019 0.001 TYR A 453 ARG 0.009 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.315 Fit side-chains REVERT: A 386 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7881 (mtmm) REVERT: A 405 ASP cc_start: 0.8611 (m-30) cc_final: 0.8317 (m-30) REVERT: A 406 GLU cc_start: 0.8990 (pt0) cc_final: 0.8685 (pt0) REVERT: B 27 LEU cc_start: 0.6422 (tp) cc_final: 0.5933 (tp) REVERT: B 45 LEU cc_start: 0.8562 (mt) cc_final: 0.8048 (mt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1569 time to fit residues: 10.2907 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 0.0270 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.0000 overall best weight: 0.4642 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.062023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.051677 restraints weight = 11601.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.053536 restraints weight = 6831.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.054959 restraints weight = 4597.957| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3008 Z= 0.197 Angle : 0.687 8.235 4111 Z= 0.355 Chirality : 0.045 0.135 452 Planarity : 0.004 0.055 540 Dihedral : 5.457 24.308 463 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -2.85 (0.40), residues: 397 helix: -3.15 (0.71), residues: 34 sheet: -1.15 (0.48), residues: 113 loop : -2.16 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 107 HIS 0.001 0.001 HIS A 519 PHE 0.013 0.001 PHE A 347 TYR 0.014 0.001 TYR A 453 ARG 0.010 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7893 (mtmm) REVERT: A 405 ASP cc_start: 0.8686 (m-30) cc_final: 0.8290 (m-30) REVERT: A 406 GLU cc_start: 0.8990 (pt0) cc_final: 0.8693 (pt0) REVERT: A 474 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6657 (tp-100) REVERT: B 45 LEU cc_start: 0.8645 (mt) cc_final: 0.8129 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1601 time to fit residues: 10.3334 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.062631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.052567 restraints weight = 11489.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054405 restraints weight = 6816.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055789 restraints weight = 4601.017| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3008 Z= 0.198 Angle : 0.696 9.032 4111 Z= 0.360 Chirality : 0.046 0.153 452 Planarity : 0.005 0.049 540 Dihedral : 5.428 24.996 463 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.75 (0.40), residues: 397 helix: -3.12 (0.73), residues: 34 sheet: -1.14 (0.48), residues: 113 loop : -2.04 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.011 0.001 PHE A 347 TYR 0.017 0.001 TYR A 453 ARG 0.011 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7877 (mtmm) REVERT: A 405 ASP cc_start: 0.8674 (m-30) cc_final: 0.8284 (m-30) REVERT: A 406 GLU cc_start: 0.8987 (pt0) cc_final: 0.8690 (pt0) REVERT: A 474 GLN cc_start: 0.6952 (tp-100) cc_final: 0.6580 (tp-100) REVERT: B 45 LEU cc_start: 0.8688 (mt) cc_final: 0.8101 (mt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1521 time to fit residues: 9.6260 Evaluate side-chains 43 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3090 r_free = 0.3090 target = 0.061721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.051862 restraints weight = 11761.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.053642 restraints weight = 7037.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054853 restraints weight = 4794.760| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3008 Z= 0.229 Angle : 0.696 9.457 4111 Z= 0.360 Chirality : 0.045 0.138 452 Planarity : 0.004 0.054 540 Dihedral : 5.498 23.957 463 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.76 (0.40), residues: 397 helix: -3.06 (0.74), residues: 34 sheet: -1.15 (0.48), residues: 113 loop : -2.06 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.012 0.001 PHE A 347 TYR 0.019 0.001 TYR A 453 ARG 0.006 0.001 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8355 (pp20) cc_final: 0.8052 (pp20) REVERT: A 386 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7889 (mtmm) REVERT: A 405 ASP cc_start: 0.8670 (m-30) cc_final: 0.8285 (m-30) REVERT: A 406 GLU cc_start: 0.8896 (pt0) cc_final: 0.8616 (pt0) REVERT: A 474 GLN cc_start: 0.6864 (tp-100) cc_final: 0.6552 (tp-100) REVERT: B 45 LEU cc_start: 0.8685 (mt) cc_final: 0.8079 (mt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1714 time to fit residues: 10.5504 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3107 r_free = 0.3107 target = 0.062551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.052833 restraints weight = 11654.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054606 restraints weight = 7041.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055616 restraints weight = 4817.610| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3008 Z= 0.193 Angle : 0.685 9.345 4111 Z= 0.354 Chirality : 0.045 0.153 452 Planarity : 0.004 0.048 540 Dihedral : 5.416 25.096 463 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.40), residues: 397 helix: -3.12 (0.71), residues: 34 sheet: -1.14 (0.48), residues: 113 loop : -2.01 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.011 0.001 PHE A 347 TYR 0.017 0.001 TYR A 453 ARG 0.007 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.81 seconds wall clock time: 23 minutes 44.53 seconds (1424.53 seconds total)