Starting phenix.real_space_refine on Sat May 10 01:11:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k19_36789/05_2025/8k19_36789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k19_36789/05_2025/8k19_36789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k19_36789/05_2025/8k19_36789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k19_36789/05_2025/8k19_36789.map" model { file = "/net/cci-nas-00/data/ceres_data/8k19_36789/05_2025/8k19_36789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k19_36789/05_2025/8k19_36789.cif" } resolution = 3.88 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= 0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1446 atoms to isotropic. 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 19 5.16 5 C 2041 2.51 5 N 546 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3224 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 906 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "B" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Time building chain proxies: 3.23, per 1000 atoms: 1.00 Number of scatterers: 3224 At special positions: 0 Unit cell: (61.48, 69.96, 94.34, 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 19 16.00 O 618 8.00 N 546 7.00 C 2041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 369.5 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 12.8% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.507A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.877A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.539A pdb=" N VAL A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 80 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.826A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 34 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 108 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.826A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 34 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.939A pdb=" N HIS B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.788A pdb=" N ALA B 84 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.658A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY E 431 " --> pdb=" O TYR E 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.658A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE E 392 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 122 hydrogen bonds defined for protein. 300 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: 0.87 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 782 1.33 - 1.46: 737 1.46 - 1.58: 1757 1.58 - 1.70: 1 1.70 - 1.82: 26 Bond restraints: 3303 Sorted by residual: bond pdb=" CB ASP B 1 " pdb=" CG ASP B 1 " ideal model delta sigma weight residual 1.516 1.631 -0.115 2.50e-02 1.60e+03 2.13e+01 bond pdb=" N GLY E 476 " pdb=" CA GLY E 476 " ideal model delta sigma weight residual 1.446 1.476 -0.030 9.50e-03 1.11e+04 1.01e+01 bond pdb=" CD2 HIS A 104 " pdb=" NE2 HIS A 104 " ideal model delta sigma weight residual 1.374 1.407 -0.033 1.10e-02 8.26e+03 8.78e+00 bond pdb=" CZ ARG B 61 " pdb=" NH2 ARG B 61 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.56e+00 bond pdb=" N VAL E 382 " pdb=" CA VAL E 382 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.18e-02 7.18e+03 8.51e+00 ... (remaining 3298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 2953 1.65 - 3.30: 1198 3.30 - 4.94: 279 4.94 - 6.59: 41 6.59 - 8.24: 13 Bond angle restraints: 4484 Sorted by residual: angle pdb=" CA ASP A 107 " pdb=" CB ASP A 107 " pdb=" CG ASP A 107 " ideal model delta sigma weight residual 112.60 119.22 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" OD1 ASN E 334 " pdb=" CG ASN E 334 " pdb=" ND2 ASN E 334 " ideal model delta sigma weight residual 122.60 116.66 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" CB HIS B 93 " pdb=" CG HIS B 93 " pdb=" CD2 HIS B 93 " ideal model delta sigma weight residual 131.20 123.49 7.71 1.30e+00 5.92e-01 3.52e+01 angle pdb=" OE1 GLN A 39 " pdb=" CD GLN A 39 " pdb=" NE2 GLN A 39 " ideal model delta sigma weight residual 122.60 117.01 5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" OE1 GLN A 13 " pdb=" CD GLN A 13 " pdb=" NE2 GLN A 13 " ideal model delta sigma weight residual 122.60 117.11 5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 4479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.54: 1886 25.54 - 51.07: 63 51.07 - 76.61: 6 76.61 - 102.15: 1 102.15 - 127.68: 1 Dihedral angle restraints: 1957 sinusoidal: 765 harmonic: 1192 Sorted by residual: dihedral pdb=" C GLU A 26 " pdb=" N GLU A 26 " pdb=" CA GLU A 26 " pdb=" CB GLU A 26 " ideal model delta harmonic sigma weight residual -122.60 -138.49 15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" CA ARG A 97 " pdb=" C ARG A 97 " pdb=" N PRO A 98 " pdb=" CA PRO A 98 " ideal model delta harmonic sigma weight residual 180.00 152.15 27.85 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASN A 32 " pdb=" C ASN A 32 " pdb=" N TYR A 33 " pdb=" CA TYR A 33 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 1954 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.112: 370 0.112 - 0.223: 105 0.223 - 0.334: 6 0.334 - 0.444: 1 0.444 - 0.555: 1 Chirality restraints: 483 Sorted by residual: chirality pdb=" CA GLU A 26 " pdb=" N GLU A 26 " pdb=" C GLU A 26 " pdb=" CB GLU A 26 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA ASN E 487 " pdb=" N ASN E 487 " pdb=" C ASN E 487 " pdb=" CB ASN E 487 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR E 523 " pdb=" CA THR E 523 " pdb=" OG1 THR E 523 " pdb=" CG2 THR E 523 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 480 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 93 " 0.135 2.00e-02 2.50e+03 1.07e-01 1.70e+02 pdb=" CG HIS B 93 " -0.115 2.00e-02 2.50e+03 pdb=" ND1 HIS B 93 " -0.115 2.00e-02 2.50e+03 pdb=" CD2 HIS B 93 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 HIS B 93 " 0.121 2.00e-02 2.50e+03 pdb=" NE2 HIS B 93 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 105 " -0.057 2.00e-02 2.50e+03 1.20e-01 1.43e+02 pdb=" CD GLU B 105 " 0.207 2.00e-02 2.50e+03 pdb=" OE1 GLU B 105 " -0.075 2.00e-02 2.50e+03 pdb=" OE2 GLU B 105 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.137 2.00e-02 2.50e+03 7.20e-02 1.04e+02 pdb=" CG TYR A 59 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " -0.093 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 1 2.18 - 2.86: 956 2.86 - 3.54: 4394 3.54 - 4.22: 7933 4.22 - 4.90: 12972 Nonbonded interactions: 26256 Sorted by model distance: nonbonded pdb=" CD2 LEU E 455 " pdb=" OE1 GLN E 493 " model vdw 1.496 3.460 nonbonded pdb=" CZ PHE E 456 " pdb=" NE2 GLN E 493 " model vdw 2.507 3.420 nonbonded pdb=" OG1 THR A 56 " pdb=" OD2 ASP E 420 " model vdw 2.538 3.040 nonbonded pdb=" OD1 ASP E 442 " pdb=" OH TYR E 451 " model vdw 2.580 3.040 nonbonded pdb=" N PHE B 49 " pdb=" O PHE B 49 " model vdw 2.586 2.496 ... (remaining 26251 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 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 : 0.014 0.115 3309 Z= 0.792 Angle : 1.836 8.239 4496 Z= 1.214 Chirality : 0.095 0.555 483 Planarity : 0.027 0.136 581 Dihedral : 13.091 127.681 1183 Min Nonbonded Distance : 1.496 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.74 % Allowed : 4.68 % Favored : 94.58 % Rotamer: Outliers : 0.57 % Allowed : 3.12 % Favored : 96.32 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 10.00 % 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: -1.84 (0.37), residues: 406 helix: -4.57 (0.30), residues: 24 sheet: -1.18 (0.39), residues: 122 loop : -0.87 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.026 TRP A 36 HIS 0.052 0.012 HIS B 93 PHE 0.078 0.013 PHE E 497 TYR 0.137 0.031 TYR A 59 ARG 0.037 0.005 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.25137 ( 107) hydrogen bonds : angle 10.11466 ( 300) SS BOND : bond 0.00853 ( 6) SS BOND : angle 1.97784 ( 12) covalent geometry : bond 0.01360 ( 3303) covalent geometry : angle 1.83568 ( 4484) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: -0.0555 (mtm) cc_final: -0.1670 (mtt) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.3745 time to fit residues: 12.7068 Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.032536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.020124 restraints weight = 51011.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.020335 restraints weight = 48011.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.020277 restraints weight = 44999.263| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3309 Z= 0.174 Angle : 0.660 6.946 4496 Z= 0.353 Chirality : 0.045 0.140 483 Planarity : 0.005 0.036 581 Dihedral : 5.583 34.216 457 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.03 (0.39), residues: 406 helix: -2.67 (0.81), residues: 32 sheet: -0.81 (0.41), residues: 128 loop : -0.22 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 109 HIS 0.003 0.001 HIS B 70 PHE 0.015 0.002 PHE B 49 TYR 0.014 0.002 TYR A 33 ARG 0.003 0.001 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 107) hydrogen bonds : angle 7.21217 ( 300) SS BOND : bond 0.00375 ( 6) SS BOND : angle 0.98619 ( 12) covalent geometry : bond 0.00390 ( 3303) covalent geometry : angle 0.65932 ( 4484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9329 (mpp) cc_final: 0.9044 (pmm) REVERT: A 82 MET cc_start: -0.0041 (mtm) cc_final: -0.0769 (mtt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3122 time to fit residues: 6.0146 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.024637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.020348 restraints weight = 73138.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.019902 restraints weight = 103040.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.019829 restraints weight = 114581.192| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3309 Z= 0.130 Angle : 0.576 5.406 4496 Z= 0.308 Chirality : 0.044 0.140 483 Planarity : 0.004 0.032 581 Dihedral : 4.877 19.448 457 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.28 % Allowed : 6.52 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.86 (0.40), residues: 406 helix: -3.37 (0.62), residues: 44 sheet: -0.30 (0.43), residues: 124 loop : -0.02 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 36 HIS 0.002 0.001 HIS A 104 PHE 0.011 0.002 PHE B 49 TYR 0.010 0.002 TYR E 365 ARG 0.004 0.001 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.02912 ( 107) hydrogen bonds : angle 6.62753 ( 300) SS BOND : bond 0.00331 ( 6) SS BOND : angle 0.98170 ( 12) covalent geometry : bond 0.00290 ( 3303) covalent geometry : angle 0.57496 ( 4484) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.2921 time to fit residues: 4.9862 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 40.0000 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 50.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.024217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.018530 restraints weight = 74432.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.018520 restraints weight = 86060.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.018520 restraints weight = 87156.497| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3309 Z= 0.140 Angle : 0.547 5.477 4496 Z= 0.296 Chirality : 0.043 0.140 483 Planarity : 0.004 0.032 581 Dihedral : 4.861 21.355 457 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.28 % Allowed : 7.08 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.80 (0.41), residues: 406 helix: -3.32 (0.64), residues: 44 sheet: -0.28 (0.43), residues: 136 loop : 0.06 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.003 0.001 HIS E 505 PHE 0.013 0.002 PHE B 49 TYR 0.015 0.002 TYR E 380 ARG 0.006 0.001 ARG E 439 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 107) hydrogen bonds : angle 6.44149 ( 300) SS BOND : bond 0.00382 ( 6) SS BOND : angle 0.95259 ( 12) covalent geometry : bond 0.00318 ( 3303) covalent geometry : angle 0.54562 ( 4484) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 0.3238 time to fit residues: 5.1847 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.0770 chunk 29 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 overall best weight: 2.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.024343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.017924 restraints weight = 73372.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.017924 restraints weight = 75812.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.017924 restraints weight = 75812.529| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3309 Z= 0.111 Angle : 0.527 6.380 4496 Z= 0.279 Chirality : 0.044 0.141 483 Planarity : 0.004 0.031 581 Dihedral : 4.611 20.683 457 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.57 % Allowed : 8.50 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.72 (0.42), residues: 406 helix: -3.45 (0.58), residues: 44 sheet: -0.16 (0.44), residues: 134 loop : 0.11 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 109 HIS 0.003 0.001 HIS B 38 PHE 0.011 0.002 PHE B 49 TYR 0.012 0.001 TYR E 380 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.02492 ( 107) hydrogen bonds : angle 6.06853 ( 300) SS BOND : bond 0.00337 ( 6) SS BOND : angle 0.83433 ( 12) covalent geometry : bond 0.00255 ( 3303) covalent geometry : angle 0.52557 ( 4484) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8651 (mpp) cc_final: 0.8406 (mpp) outliers start: 2 outliers final: 1 residues processed: 13 average time/residue: 0.3377 time to fit residues: 5.3647 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 50.0000 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS E 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.023915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.017483 restraints weight = 74823.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.017460 restraints weight = 78644.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.017460 restraints weight = 80326.042| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3309 Z= 0.163 Angle : 0.568 5.900 4496 Z= 0.305 Chirality : 0.044 0.142 483 Planarity : 0.004 0.034 581 Dihedral : 4.842 21.623 457 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.70 % Allowed : 9.63 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.74 (0.42), residues: 406 helix: -3.60 (0.56), residues: 44 sheet: -0.29 (0.43), residues: 142 loop : 0.24 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 109 HIS 0.004 0.001 HIS B 38 PHE 0.013 0.002 PHE E 374 TYR 0.013 0.002 TYR E 380 ARG 0.004 0.000 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 107) hydrogen bonds : angle 6.62729 ( 300) SS BOND : bond 0.00425 ( 6) SS BOND : angle 1.35182 ( 12) covalent geometry : bond 0.00369 ( 3303) covalent geometry : angle 0.56408 ( 4484) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: -0.2723 (mmt) cc_final: -0.3790 (mtt) outliers start: 6 outliers final: 1 residues processed: 16 average time/residue: 0.2165 time to fit residues: 4.5138 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 40.0000 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.023552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.017820 restraints weight = 73613.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.017632 restraints weight = 86792.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.017632 restraints weight = 98250.129| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 3309 Z= 0.196 Angle : 0.604 7.420 4496 Z= 0.327 Chirality : 0.044 0.143 483 Planarity : 0.005 0.038 581 Dihedral : 5.232 21.761 457 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 27.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.85 % Allowed : 11.05 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.85 (0.43), residues: 406 helix: -3.52 (0.60), residues: 44 sheet: -0.46 (0.43), residues: 143 loop : 0.22 (0.45), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 47 HIS 0.006 0.002 HIS B 38 PHE 0.013 0.002 PHE E 347 TYR 0.018 0.002 TYR E 380 ARG 0.004 0.001 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 107) hydrogen bonds : angle 6.70335 ( 300) SS BOND : bond 0.00665 ( 6) SS BOND : angle 0.95939 ( 12) covalent geometry : bond 0.00432 ( 3303) covalent geometry : angle 0.60234 ( 4484) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: -0.2182 (mmt) cc_final: -0.3454 (mtt) REVERT: A 100 MET cc_start: 0.5574 (ttt) cc_final: 0.5018 (ttt) outliers start: 3 outliers final: 2 residues processed: 13 average time/residue: 0.2498 time to fit residues: 4.1745 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 50.0000 chunk 35 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 10 optimal weight: 50.0000 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 34 optimal weight: 0.4980 overall best weight: 5.0986 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.023224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.016730 restraints weight = 75246.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.016728 restraints weight = 78502.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.016728 restraints weight = 78645.263| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.7413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 3309 Z= 0.148 Angle : 0.568 8.020 4496 Z= 0.302 Chirality : 0.044 0.149 483 Planarity : 0.004 0.038 581 Dihedral : 5.093 21.194 457 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.85 % Allowed : 12.75 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.79 (0.43), residues: 406 helix: -3.44 (0.62), residues: 44 sheet: -0.35 (0.44), residues: 142 loop : 0.17 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.006 0.002 HIS B 38 PHE 0.012 0.002 PHE B 49 TYR 0.017 0.002 TYR E 380 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.02822 ( 107) hydrogen bonds : angle 6.38425 ( 300) SS BOND : bond 0.00392 ( 6) SS BOND : angle 0.87041 ( 12) covalent geometry : bond 0.00340 ( 3303) covalent geometry : angle 0.56710 ( 4484) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9494 (tptp) cc_final: 0.9220 (tttt) REVERT: A 82 MET cc_start: 0.0870 (mmt) cc_final: -0.0206 (mtt) outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.2929 time to fit residues: 5.1600 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 overall best weight: 3.3590 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.023176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.016094 restraints weight = 75133.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.016205 restraints weight = 68693.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.016285 restraints weight = 64158.025| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.7448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 3309 Z= 0.124 Angle : 0.560 6.894 4496 Z= 0.299 Chirality : 0.043 0.141 483 Planarity : 0.004 0.038 581 Dihedral : 4.985 21.000 457 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.13 % Allowed : 12.46 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.73 (0.44), residues: 406 helix: -3.47 (0.63), residues: 44 sheet: -0.38 (0.43), residues: 144 loop : 0.30 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.006 0.001 HIS B 38 PHE 0.011 0.001 PHE B 49 TYR 0.013 0.001 TYR E 380 ARG 0.002 0.000 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.02693 ( 107) hydrogen bonds : angle 6.01118 ( 300) SS BOND : bond 0.00401 ( 6) SS BOND : angle 0.94828 ( 12) covalent geometry : bond 0.00295 ( 3303) covalent geometry : angle 0.55880 ( 4484) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5987 (mmt) cc_final: 0.5678 (mtt) outliers start: 4 outliers final: 2 residues processed: 13 average time/residue: 0.2600 time to fit residues: 4.2736 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 50.0000 chunk 27 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 19 optimal weight: 40.0000 chunk 4 optimal weight: 40.0000 chunk 5 optimal weight: 30.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.023200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.016852 restraints weight = 73476.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.016852 restraints weight = 78733.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.016852 restraints weight = 78733.395| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.7903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3309 Z= 0.162 Angle : 0.575 7.308 4496 Z= 0.311 Chirality : 0.044 0.144 483 Planarity : 0.005 0.038 581 Dihedral : 5.032 21.937 457 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.85 % Allowed : 12.46 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.77 (0.44), residues: 406 helix: -3.40 (0.64), residues: 44 sheet: -0.47 (0.42), residues: 142 loop : 0.30 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.006 0.002 HIS B 38 PHE 0.012 0.002 PHE E 347 TYR 0.014 0.002 TYR E 365 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 107) hydrogen bonds : angle 6.26093 ( 300) SS BOND : bond 0.00420 ( 6) SS BOND : angle 0.74898 ( 12) covalent geometry : bond 0.00371 ( 3303) covalent geometry : angle 0.57408 ( 4484) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8622 (ppp) cc_final: 0.7927 (ppp) REVERT: A 82 MET cc_start: -0.2492 (mmt) cc_final: -0.3697 (mtt) outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.2411 time to fit residues: 3.8481 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 446 THR 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 30 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.023140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.018123 restraints weight = 72621.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.018123 restraints weight = 82909.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.018123 restraints weight = 82909.429| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.7893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3309 Z= 0.129 Angle : 0.595 9.071 4496 Z= 0.310 Chirality : 0.044 0.140 483 Planarity : 0.004 0.038 581 Dihedral : 4.887 21.099 457 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.85 % Allowed : 12.75 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.80 (0.44), residues: 406 helix: -3.46 (0.64), residues: 44 sheet: -0.50 (0.41), residues: 143 loop : 0.29 (0.48), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.006 0.002 HIS B 38 PHE 0.013 0.002 PHE E 456 TYR 0.014 0.001 TYR E 380 ARG 0.004 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.02638 ( 107) hydrogen bonds : angle 6.12423 ( 300) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.65214 ( 12) covalent geometry : bond 0.00303 ( 3303) covalent geometry : angle 0.59472 ( 4484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.62 seconds wall clock time: 29 minutes 5.58 seconds (1745.58 seconds total)