Starting phenix.real_space_refine on Fri Jul 3 13:30:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lys_23600/07_2026/7lys_23600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lys_23600/07_2026/7lys_23600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lys_23600/07_2026/7lys_23600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lys_23600/07_2026/7lys_23600.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lys_23600/07_2026/7lys_23600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lys_23600/07_2026/7lys_23600.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lys_23600/07_2026/7lys_23600.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lys_23600/07_2026/7lys_23600.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.171 sd= 1.109 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 899 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: 6 Type Number sf(0) Gaussians P 88 5.49 5 S 14 5.16 5 C 4232 2.51 5 N 1313 2.21 5 O 1552 1.98 5 H 6374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 10734 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 39, 'TRANS': 629} Chain breaks: 2 Chain: "B" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1323 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 948 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Time building chain proxies: 2.19, per 1000 atoms: 0.16 Number of scatterers: 13573 At special positions: 0 Unit cell: (84.74, 99.235, 125.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 88 15.00 O 1552 8.00 N 1313 7.00 C 4232 6.00 H 6374 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 369.4 milliseconds 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 48.7% alpha, 9.4% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 39 Processing helix chain 'A' and resid 40 through 48 removed outlier: 4.311A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 125 through 169 removed outlier: 3.648A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.740A pdb=" N ARG A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.194A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.838A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 483 removed outlier: 5.461A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 549 through 566 Processing helix chain 'A' and resid 568 through 597 removed outlier: 3.531A pdb=" N LYS A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 636 through 651 removed outlier: 4.347A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199 removed outlier: 5.741A pdb=" N VAL A 66 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP A 312 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.313A pdb=" N LEU A 370 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 391 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 606 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU A 395 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 388 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.562A pdb=" N VAL A 533 " --> pdb=" O PHE A 517 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6365 1.03 - 1.23: 51 1.23 - 1.42: 3348 1.42 - 1.62: 4126 1.62 - 1.81: 19 Bond restraints: 13909 Sorted by residual: bond pdb=" C1' DT D 1 " pdb=" N1 DT D 1 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.38e+00 bond pdb=" C1' DC D 6 " pdb=" N1 DC D 6 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.56e+00 bond pdb=" C1' DC D -9 " pdb=" N1 DC D -9 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.43e+00 bond pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.89e+00 bond pdb=" C1' DT C 0 " pdb=" N1 DT C 0 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.83e+00 ... (remaining 13904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 21599 0.83 - 1.66: 2885 1.66 - 2.48: 462 2.48 - 3.31: 170 3.31 - 4.14: 31 Bond angle restraints: 25147 Sorted by residual: angle pdb=" N3 DT C -14 " pdb=" C4 DT C -14 " pdb=" O4 DT C -14 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 0 " pdb=" C4 DT C 0 " pdb=" O4 DT C 0 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C -9 " pdb=" C4 DT C -9 " pdb=" O4 DT C -9 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 25142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 5887 33.78 - 67.57: 344 67.57 - 101.35: 9 101.35 - 135.13: 0 135.13 - 168.92: 2 Dihedral angle restraints: 6242 sinusoidal: 3984 harmonic: 2258 Sorted by residual: dihedral pdb=" CA PRO A 171 " pdb=" C PRO A 171 " pdb=" N GLU A 172 " pdb=" CA GLU A 172 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL A 236 " pdb=" C VAL A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE A 653 " pdb=" C PHE A 653 " pdb=" N TYR A 654 " pdb=" CA TYR A 654 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 910 0.037 - 0.075: 187 0.075 - 0.112: 52 0.112 - 0.150: 26 0.150 - 0.187: 32 Chirality restraints: 1207 Sorted by residual: chirality pdb=" C3' DA C -7 " pdb=" C4' DA C -7 " pdb=" O3' DA C -7 " pdb=" C2' DA C -7 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" C3' DC C -6 " pdb=" C4' DC C -6 " pdb=" O3' DC C -6 " pdb=" C2' DC C -6 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" C3' DT C -9 " pdb=" C4' DT C -9 " pdb=" O3' DT C -9 " pdb=" C2' DT C -9 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 1204 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 620 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 621 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 60 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.09e-01 pdb=" N PRO A 61 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 614 " 0.007 2.00e-02 2.50e+03 6.11e-03 8.39e-01 pdb=" CG HIS A 614 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 614 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 614 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 614 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS A 614 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 614 " -0.001 2.00e-02 2.50e+03 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 815 2.20 - 2.80: 25702 2.80 - 3.40: 35520 3.40 - 4.00: 47770 4.00 - 4.60: 71518 Nonbonded interactions: 181325 Sorted by model distance: nonbonded pdb=" OD1 ASN A 183 " pdb=" H GLU A 184 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLN A 386 " pdb=" H GLN A 386 " model vdw 1.625 2.450 nonbonded pdb="HH12 ARG A 582 " pdb=" OP2 G B 2 " model vdw 1.626 2.450 nonbonded pdb=" HZ1 LYS A 536 " pdb=" O5' DG C -18 " model vdw 1.636 2.450 nonbonded pdb=" HH TYR A 123 " pdb=" OH TYR A 201 " model vdw 1.679 2.450 ... (remaining 181320 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.100 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 15.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.004 0.041 7535 Z= 0.293 Angle : 0.608 4.141 10601 Z= 0.435 Chirality : 0.046 0.187 1207 Planarity : 0.003 0.032 1048 Dihedral : 17.888 168.916 3094 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.30), residues: 663 helix: -0.22 (0.29), residues: 295 sheet: -1.50 (0.55), residues: 74 loop : -1.52 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 538 TYR 0.010 0.001 TYR A 201 PHE 0.015 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.29 ( 7535) covalent geometry : angle 0.60821 / 0.43 (10601) hydrogen bonds : bond 0.21570 / 14.33 ( 344) hydrogen bonds : angle 7.08980 / 5.15 ( 910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 ILE cc_start: 0.9280 (mm) cc_final: 0.9040 (mt) REVERT: A 659 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8245 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2091 time to fit residues: 24.7974 Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 650 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 = 0.3126 r_free = 0.3126 target = 0.076200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066478 restraints weight = 43457.646| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.69 r_work: 0.2843 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7535 Z= 0.157 Angle : 0.601 5.297 10601 Z= 0.342 Chirality : 0.041 0.202 1207 Planarity : 0.004 0.040 1048 Dihedral : 18.448 172.811 1758 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.17 % Allowed : 10.30 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.32), residues: 663 helix: 0.67 (0.30), residues: 306 sheet: -1.36 (0.57), residues: 74 loop : -1.13 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.008 0.001 TYR A 654 PHE 0.017 0.001 PHE A 354 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 ( 7535) covalent geometry : angle 0.60078 / 0.34 (10601) hydrogen bonds : bond 0.06160 / 4.10 ( 344) hydrogen bonds : angle 5.08680 / 3.66 ( 910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8626 (ttm170) cc_final: 0.8422 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.2437 time to fit residues: 23.2503 Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 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 = 0.3118 r_free = 0.3118 target = 0.075815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.066036 restraints weight = 43944.736| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.68 r_work: 0.2835 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7535 Z= 0.176 Angle : 0.574 6.082 10601 Z= 0.326 Chirality : 0.040 0.211 1207 Planarity : 0.004 0.040 1048 Dihedral : 18.492 174.272 1758 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.87 % Allowed : 10.82 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.33), residues: 663 helix: 1.08 (0.30), residues: 306 sheet: -1.45 (0.58), residues: 74 loop : -1.00 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 547 TYR 0.009 0.001 TYR A 654 PHE 0.020 0.001 PHE A 354 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 ( 7535) covalent geometry : angle 0.57399 / 0.33 (10601) hydrogen bonds : bond 0.05254 / 3.56 ( 344) hydrogen bonds : angle 4.68999 / 3.39 ( 910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 284 ARG cc_start: 0.8669 (ttm170) cc_final: 0.8377 (mtt-85) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.2479 time to fit residues: 23.8395 Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 0.0070 chunk 71 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.076923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.067214 restraints weight = 43530.685| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.68 r_work: 0.2854 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7535 Z= 0.131 Angle : 0.544 5.384 10601 Z= 0.309 Chirality : 0.039 0.207 1207 Planarity : 0.004 0.050 1048 Dihedral : 18.504 175.099 1758 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.35 % Allowed : 11.69 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.33), residues: 663 helix: 1.47 (0.31), residues: 304 sheet: -1.62 (0.54), residues: 81 loop : -0.82 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 547 TYR 0.010 0.001 TYR A 654 PHE 0.012 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 7535) covalent geometry : angle 0.54387 / 0.31 (10601) hydrogen bonds : bond 0.04554 / 3.11 ( 344) hydrogen bonds : angle 4.43274 / 3.22 ( 910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8665 (ttm170) cc_final: 0.8361 (mtt-85) outliers start: 2 outliers final: 2 residues processed: 75 average time/residue: 0.2465 time to fit residues: 23.3577 Evaluate side-chains 70 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.075926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.066149 restraints weight = 44137.920| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.68 r_work: 0.2832 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7535 Z= 0.168 Angle : 0.544 5.436 10601 Z= 0.310 Chirality : 0.039 0.212 1207 Planarity : 0.004 0.038 1048 Dihedral : 18.504 174.361 1758 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.70 % Allowed : 12.57 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.33), residues: 663 helix: 1.63 (0.31), residues: 304 sheet: -1.77 (0.53), residues: 79 loop : -0.73 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 512 TYR 0.009 0.001 TYR A 654 PHE 0.013 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 ( 7535) covalent geometry : angle 0.54401 / 0.31 (10601) hydrogen bonds : bond 0.04534 / 3.09 ( 344) hydrogen bonds : angle 4.29856 / 3.13 ( 910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8414 (mtt-85) outliers start: 4 outliers final: 4 residues processed: 73 average time/residue: 0.2581 time to fit residues: 23.9072 Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.066461 restraints weight = 43504.833| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.69 r_work: 0.2846 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7535 Z= 0.175 Angle : 0.551 5.794 10601 Z= 0.312 Chirality : 0.040 0.217 1207 Planarity : 0.004 0.064 1048 Dihedral : 18.523 174.030 1758 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.87 % Allowed : 13.79 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.34), residues: 663 helix: 1.73 (0.31), residues: 304 sheet: -1.82 (0.54), residues: 72 loop : -0.60 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.010 0.001 TYR A 654 PHE 0.013 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 ( 7535) covalent geometry : angle 0.55145 / 0.31 (10601) hydrogen bonds : bond 0.04384 / 2.99 ( 344) hydrogen bonds : angle 4.20204 / 3.06 ( 910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8554 (mtm-85) REVERT: A 284 ARG cc_start: 0.8738 (ttm170) cc_final: 0.8474 (mtt-85) REVERT: A 295 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8778 (mm-40) outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.2531 time to fit residues: 23.9932 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.066554 restraints weight = 43223.673| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.67 r_work: 0.2845 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7535 Z= 0.173 Angle : 0.545 5.944 10601 Z= 0.309 Chirality : 0.039 0.219 1207 Planarity : 0.004 0.039 1048 Dihedral : 18.533 173.443 1758 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.22 % Allowed : 13.79 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.34), residues: 663 helix: 1.78 (0.31), residues: 305 sheet: -1.85 (0.53), residues: 74 loop : -0.60 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 575 TYR 0.010 0.001 TYR A 654 PHE 0.013 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 ( 7535) covalent geometry : angle 0.54529 / 0.31 (10601) hydrogen bonds : bond 0.04342 / 2.96 ( 344) hydrogen bonds : angle 4.13544 / 3.02 ( 910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8343 (tp) REVERT: A 139 ARG cc_start: 0.8835 (mtm-85) cc_final: 0.8533 (mtm-85) REVERT: A 284 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8464 (mtt-85) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.2198 time to fit residues: 20.9402 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.076300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.066674 restraints weight = 43096.728| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.67 r_work: 0.2845 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7535 Z= 0.164 Angle : 0.543 5.484 10601 Z= 0.307 Chirality : 0.039 0.220 1207 Planarity : 0.004 0.038 1048 Dihedral : 18.528 173.329 1758 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.22 % Allowed : 14.31 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.34), residues: 663 helix: 1.83 (0.31), residues: 305 sheet: -1.81 (0.53), residues: 74 loop : -0.59 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.011 0.001 TYR A 654 PHE 0.012 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 7535) covalent geometry : angle 0.54331 / 0.31 (10601) hydrogen bonds : bond 0.04248 / 2.90 ( 344) hydrogen bonds : angle 4.10311 / 2.99 ( 910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 139 ARG cc_start: 0.8846 (mtm-85) cc_final: 0.8551 (mtm-85) REVERT: A 284 ARG cc_start: 0.8735 (ttm170) cc_final: 0.8457 (mtt-85) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.2322 time to fit residues: 21.9579 Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.066249 restraints weight = 43472.814| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.68 r_work: 0.2838 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7535 Z= 0.186 Angle : 0.552 6.592 10601 Z= 0.312 Chirality : 0.040 0.222 1207 Planarity : 0.005 0.065 1048 Dihedral : 18.538 173.031 1758 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.22 % Allowed : 14.83 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.34), residues: 663 helix: 1.84 (0.31), residues: 305 sheet: -1.79 (0.53), residues: 74 loop : -0.59 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 422 TYR 0.011 0.001 TYR A 654 PHE 0.013 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 ( 7535) covalent geometry : angle 0.55237 / 0.31 (10601) hydrogen bonds : bond 0.04283 / 2.92 ( 344) hydrogen bonds : angle 4.08809 / 2.98 ( 910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8276 (tp) REVERT: A 284 ARG cc_start: 0.8735 (ttm170) cc_final: 0.8438 (mtt-85) REVERT: A 295 GLN cc_start: 0.8890 (mm110) cc_final: 0.8659 (mm-40) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.2050 time to fit residues: 19.3912 Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.076470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.066792 restraints weight = 43032.371| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.65 r_work: 0.2852 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7535 Z= 0.140 Angle : 0.536 6.367 10601 Z= 0.303 Chirality : 0.039 0.220 1207 Planarity : 0.004 0.042 1048 Dihedral : 18.522 172.929 1758 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.87 % Allowed : 15.36 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.34), residues: 663 helix: 1.91 (0.31), residues: 305 sheet: -1.74 (0.54), residues: 74 loop : -0.53 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.011 0.001 TYR A 654 PHE 0.012 0.001 PHE A 613 TRP 0.007 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 7535) covalent geometry : angle 0.53628 / 0.30 (10601) hydrogen bonds : bond 0.04121 / 2.81 ( 344) hydrogen bonds : angle 4.04562 / 2.95 ( 910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8286 (tp) REVERT: A 139 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8533 (mtm-85) REVERT: A 284 ARG cc_start: 0.8720 (ttm170) cc_final: 0.8442 (mtt-85) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 0.2489 time to fit residues: 22.8015 Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.0670 chunk 8 optimal weight: 0.0570 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 14 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.068589 restraints weight = 43409.692| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.66 r_work: 0.2885 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7535 Z= 0.117 Angle : 0.522 6.532 10601 Z= 0.295 Chirality : 0.038 0.218 1207 Planarity : 0.004 0.041 1048 Dihedral : 18.472 172.855 1758 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.52 % Allowed : 15.71 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.34), residues: 663 helix: 2.03 (0.31), residues: 305 sheet: -1.62 (0.55), residues: 74 loop : -0.47 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 155 TYR 0.011 0.001 TYR A 654 PHE 0.011 0.001 PHE A 613 TRP 0.008 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 ( 7535) covalent geometry : angle 0.52205 / 0.30 (10601) hydrogen bonds : bond 0.03938 / 2.68 ( 344) hydrogen bonds : angle 3.98112 / 2.90 ( 910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.06 seconds wall clock time: 55 minutes 54.22 seconds (3354.22 seconds total)