Starting phenix.real_space_refine on Wed Jul 1 22:41:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw9_39626/07_2026/8yw9_39626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw9_39626/07_2026/8yw9_39626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yw9_39626/07_2026/8yw9_39626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw9_39626/07_2026/8yw9_39626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yw9_39626/07_2026/8yw9_39626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw9_39626/07_2026/8yw9_39626.map" } resolution = 3.01 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= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 21 5.16 5 C 2391 2.51 5 N 630 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s 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: 3709 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 984 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain: "A" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 754 Classifications: {'peptide': 94} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 89} Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1003 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 1.13, per 1000 atoms: 0.30 Number of scatterers: 3709 At special positions: 0 Unit cell: (82.08, 98.04, 96.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 2 15.00 O 665 8.00 N 630 7.00 C 2391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 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: 0.34 Conformation dependent library (CDL) restraints added in 143.8 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 46.3% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.718A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 68 through 89 removed outlier: 3.974A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 126 Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 24 through 34 Proline residue: A 30 - end of helix removed outlier: 3.595A pdb=" N TRP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 removed outlier: 3.588A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.632A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.229A pdb=" N GLY C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER C 126 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 12 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.229A pdb=" N GLY C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER C 126 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 12 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.404A pdb=" N GLY D 10 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER D 114 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL D 12 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.404A pdb=" N GLY D 10 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER D 114 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL D 12 " --> pdb=" O SER D 114 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 582 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: 0.48 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 563 1.29 - 1.42: 1082 1.42 - 1.55: 2099 1.55 - 1.68: 25 1.68 - 1.80: 36 Bond restraints: 3805 Sorted by residual: bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.333 1.444 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.339 1.432 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C60 CDL B 201 " pdb=" C61 CDL B 201 " ideal model delta sigma weight residual 1.527 1.603 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 3800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 5034 2.97 - 5.94: 89 5.94 - 8.91: 4 8.91 - 11.88: 3 11.88 - 14.85: 4 Bond angle restraints: 5134 Sorted by residual: angle pdb=" OA3 CDL B 201 " pdb=" PA1 CDL B 201 " pdb=" OA4 CDL B 201 " ideal model delta sigma weight residual 121.92 107.07 14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " pdb=" OB5 CDL B 201 " ideal model delta sigma weight residual 96.70 110.16 -13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C31 CDL B 201 " pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 110.96 123.77 -12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" OB3 CDL B 201 " pdb=" PB2 CDL B 201 " pdb=" OB4 CDL B 201 " ideal model delta sigma weight residual 121.80 109.01 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" N ASP D 52 " pdb=" CA ASP D 52 " pdb=" C ASP D 52 " ideal model delta sigma weight residual 110.35 115.73 -5.38 1.38e+00 5.25e-01 1.52e+01 ... (remaining 5129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 1988 17.84 - 35.68: 177 35.68 - 53.52: 74 53.52 - 71.36: 25 71.36 - 89.20: 2 Dihedral angle restraints: 2266 sinusoidal: 951 harmonic: 1315 Sorted by residual: dihedral pdb=" C ASP D 52 " pdb=" N ASP D 52 " pdb=" CA ASP D 52 " pdb=" CB ASP D 52 " ideal model delta harmonic sigma weight residual -122.60 -131.96 9.36 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" CA TYR C 32 " pdb=" C TYR C 32 " pdb=" N ALA C 33 " pdb=" CA ALA C 33 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLY C 35 " pdb=" C GLY C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta harmonic sigma weight residual 180.00 163.93 16.07 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 426 0.058 - 0.116: 69 0.116 - 0.175: 24 0.175 - 0.233: 7 0.233 - 0.291: 1 Chirality restraints: 527 Sorted by residual: chirality pdb=" CA ASP D 52 " pdb=" N ASP D 52 " pdb=" C ASP D 52 " pdb=" CB ASP D 52 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA GLU C 105 " pdb=" N GLU C 105 " pdb=" C GLU C 105 " pdb=" CB GLU C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA GLN D 54 " pdb=" N GLN D 54 " pdb=" C GLN D 54 " pdb=" CB GLN D 54 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 524 not shown) Planarity restraints: 640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 51 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C ILE C 51 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE C 51 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG C 52 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 45 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 46 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 103 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C TYR C 103 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR C 103 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR C 104 " 0.009 2.00e-02 2.50e+03 ... (remaining 637 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1044 2.81 - 3.33: 3163 3.33 - 3.86: 6199 3.86 - 4.38: 7509 4.38 - 4.90: 12546 Nonbonded interactions: 30461 Sorted by model distance: nonbonded pdb=" O SER A 108 " pdb=" OG SER A 108 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.365 3.040 nonbonded pdb=" OE2 GLU C 6 " pdb=" N CYS C 96 " model vdw 2.386 3.120 nonbonded pdb=" OB6 CDL B 201 " pdb=" OB8 CDL B 201 " model vdw 2.408 2.432 nonbonded pdb=" O LYS A 100 " pdb=" OG1 THR A 104 " model vdw 2.430 3.040 ... (remaining 30456 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: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.009 0.111 3807 Z= 0.507 Angle : 1.021 14.853 5138 Z= 0.596 Chirality : 0.056 0.291 527 Planarity : 0.004 0.040 640 Dihedral : 16.933 89.203 1428 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.81 % Allowed : 12.67 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.99 (0.37), residues: 450 helix: -0.25 (0.37), residues: 170 sheet: -0.75 (0.42), residues: 130 loop : -0.73 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.014 0.001 TYR A 62 PHE 0.011 0.002 PHE A 81 TRP 0.007 0.001 TRP B 82 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.51 ( 3805) covalent geometry : angle 1.01779 / 0.59 ( 5134) SS BOND : bond 0.00462 / 0.26 ( 2) SS BOND : angle 3.20884 / 1.62 ( 4) hydrogen bonds : bond 0.13872 / 9.09 ( 210) hydrogen bonds : angle 6.56224 / 4.71 ( 582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: B 86 SER cc_start: 0.9141 (p) cc_final: 0.8841 (m) REVERT: C 31 HIS cc_start: 0.5083 (m-70) cc_final: 0.4834 (m-70) outliers start: 3 outliers final: 0 residues processed: 40 average time/residue: 0.0835 time to fit residues: 4.1454 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 94 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.193906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110857 restraints weight = 3775.240| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.51 r_work: 0.2966 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3807 Z= 0.172 Angle : 0.497 5.566 5138 Z= 0.266 Chirality : 0.041 0.127 527 Planarity : 0.004 0.034 640 Dihedral : 12.801 59.793 610 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.70 % Allowed : 12.94 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.42 (0.39), residues: 450 helix: 1.12 (0.40), residues: 171 sheet: -0.23 (0.41), residues: 133 loop : 0.01 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 50 TYR 0.018 0.001 TYR C 98 PHE 0.008 0.001 PHE A 69 TRP 0.006 0.001 TRP C 110 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 3805) covalent geometry : angle 0.49642 / 0.27 ( 5134) SS BOND : bond 0.00167 / 0.10 ( 2) SS BOND : angle 0.81122 / 0.44 ( 4) hydrogen bonds : bond 0.03755 / 2.65 ( 210) hydrogen bonds : angle 4.90344 / 3.55 ( 582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: B 86 SER cc_start: 0.9268 (p) cc_final: 0.8939 (m) outliers start: 10 outliers final: 7 residues processed: 38 average time/residue: 0.0487 time to fit residues: 2.4372 Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS ** C 31 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 = 0.4064 r_free = 0.4064 target = 0.193026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107994 restraints weight = 3740.501| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.58 r_work: 0.2951 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3807 Z= 0.167 Angle : 0.466 5.620 5138 Z= 0.247 Chirality : 0.040 0.127 527 Planarity : 0.004 0.027 640 Dihedral : 11.769 59.719 610 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.43 % Allowed : 13.48 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.94 (0.40), residues: 450 helix: 1.55 (0.40), residues: 172 sheet: 0.14 (0.44), residues: 120 loop : 0.16 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.012 0.001 TYR C 98 PHE 0.008 0.001 PHE A 69 TRP 0.006 0.001 TRP C 110 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 3805) covalent geometry : angle 0.46512 / 0.25 ( 5134) SS BOND : bond 0.00052 / 0.03 ( 2) SS BOND : angle 0.86969 / 0.42 ( 4) hydrogen bonds : bond 0.03545 / 2.53 ( 210) hydrogen bonds : angle 4.55124 / 3.28 ( 582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8687 (m-40) cc_final: 0.8433 (m110) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.0665 time to fit residues: 3.1646 Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 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 = 0.4066 r_free = 0.4066 target = 0.193201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.108390 restraints weight = 3721.191| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.56 r_work: 0.2956 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3807 Z= 0.159 Angle : 0.456 5.621 5138 Z= 0.242 Chirality : 0.040 0.125 527 Planarity : 0.003 0.028 640 Dihedral : 10.784 59.699 610 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.96 % Allowed : 12.67 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.21 (0.40), residues: 450 helix: 1.75 (0.40), residues: 172 sheet: 0.30 (0.45), residues: 120 loop : 0.31 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 10 TYR 0.012 0.001 TYR A 62 PHE 0.007 0.001 PHE A 69 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 3805) covalent geometry : angle 0.45608 / 0.24 ( 5134) SS BOND : bond 0.00082 / 0.05 ( 2) SS BOND : angle 0.79388 / 0.39 ( 4) hydrogen bonds : bond 0.03404 / 2.43 ( 210) hydrogen bonds : angle 4.34219 / 3.12 ( 582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8662 (m-40) cc_final: 0.8420 (m110) outliers start: 11 outliers final: 7 residues processed: 34 average time/residue: 0.0572 time to fit residues: 2.5879 Evaluate side-chains 32 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 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 = 0.4070 r_free = 0.4070 target = 0.193339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110261 restraints weight = 3709.339| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.47 r_work: 0.2973 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3807 Z= 0.148 Angle : 0.441 5.601 5138 Z= 0.233 Chirality : 0.040 0.126 527 Planarity : 0.003 0.029 640 Dihedral : 10.716 59.714 610 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.16 % Allowed : 13.48 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.45 (0.40), residues: 450 helix: 1.89 (0.40), residues: 172 sheet: 0.50 (0.45), residues: 120 loop : 0.45 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 10 TYR 0.012 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 3805) covalent geometry : angle 0.44097 / 0.23 ( 5134) SS BOND : bond 0.00080 / 0.05 ( 2) SS BOND : angle 0.66923 / 0.31 ( 4) hydrogen bonds : bond 0.03335 / 2.38 ( 210) hydrogen bonds : angle 4.22606 / 3.04 ( 582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8608 (m-40) cc_final: 0.8385 (m110) outliers start: 8 outliers final: 8 residues processed: 37 average time/residue: 0.0518 time to fit residues: 2.4773 Evaluate side-chains 38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.195483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111188 restraints weight = 3779.605| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.57 r_work: 0.2996 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3807 Z= 0.114 Angle : 0.414 5.475 5138 Z= 0.219 Chirality : 0.039 0.121 527 Planarity : 0.003 0.030 640 Dihedral : 10.401 59.970 610 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.62 % Allowed : 14.82 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.75 (0.41), residues: 450 helix: 2.16 (0.40), residues: 172 sheet: 0.73 (0.46), residues: 120 loop : 0.51 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.010 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.002 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 3805) covalent geometry : angle 0.41427 / 0.22 ( 5134) SS BOND : bond 0.00151 / 0.09 ( 2) SS BOND : angle 0.42223 / 0.20 ( 4) hydrogen bonds : bond 0.03084 / 2.19 ( 210) hydrogen bonds : angle 4.00978 / 2.88 ( 582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8577 (m-40) cc_final: 0.8366 (m110) REVERT: D 97 LYS cc_start: 0.7573 (tttp) cc_final: 0.7256 (tttp) outliers start: 6 outliers final: 5 residues processed: 34 average time/residue: 0.0718 time to fit residues: 3.1034 Evaluate side-chains 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.0050 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.196756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112927 restraints weight = 3822.445| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.56 r_work: 0.3016 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3807 Z= 0.096 Angle : 0.399 5.400 5138 Z= 0.211 Chirality : 0.038 0.120 527 Planarity : 0.003 0.030 640 Dihedral : 10.178 59.368 610 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.08 % Allowed : 15.90 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.04 (0.41), residues: 450 helix: 2.42 (0.39), residues: 172 sheet: 0.90 (0.46), residues: 120 loop : 0.64 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.010 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.002 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 3805) covalent geometry : angle 0.39896 / 0.21 ( 5134) SS BOND : bond 0.00168 / 0.10 ( 2) SS BOND : angle 0.33543 / 0.16 ( 4) hydrogen bonds : bond 0.02968 / 2.10 ( 210) hydrogen bonds : angle 3.84748 / 2.77 ( 582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8557 (m-40) cc_final: 0.8327 (m110) outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.0747 time to fit residues: 2.8601 Evaluate side-chains 30 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 0.0270 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.197505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113485 restraints weight = 3808.134| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.57 r_work: 0.3024 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3807 Z= 0.094 Angle : 0.396 5.386 5138 Z= 0.209 Chirality : 0.038 0.119 527 Planarity : 0.003 0.029 640 Dihedral : 10.049 58.937 610 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.62 % Allowed : 15.90 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.22 (0.41), residues: 450 helix: 2.58 (0.39), residues: 172 sheet: 1.00 (0.43), residues: 130 loop : 0.71 (0.57), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.009 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.002 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 ( 3805) covalent geometry : angle 0.39625 / 0.21 ( 5134) SS BOND : bond 0.00170 / 0.10 ( 2) SS BOND : angle 0.32751 / 0.16 ( 4) hydrogen bonds : bond 0.02937 / 2.08 ( 210) hydrogen bonds : angle 3.74556 / 2.70 ( 582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8561 (m-40) cc_final: 0.8360 (m110) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.0742 time to fit residues: 3.0387 Evaluate side-chains 31 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.196042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112947 restraints weight = 3761.132| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.51 r_work: 0.3010 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3807 Z= 0.109 Angle : 0.403 5.459 5138 Z= 0.213 Chirality : 0.039 0.121 527 Planarity : 0.003 0.029 640 Dihedral : 10.059 58.549 610 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 15.09 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.23 (0.40), residues: 450 helix: 2.51 (0.39), residues: 172 sheet: 1.02 (0.43), residues: 130 loop : 0.79 (0.57), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.011 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 3805) covalent geometry : angle 0.40291 / 0.21 ( 5134) SS BOND : bond 0.00147 / 0.09 ( 2) SS BOND : angle 0.38521 / 0.18 ( 4) hydrogen bonds : bond 0.03052 / 2.17 ( 210) hydrogen bonds : angle 3.77853 / 2.72 ( 582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8550 (m-40) cc_final: 0.8326 (m110) outliers start: 5 outliers final: 5 residues processed: 31 average time/residue: 0.0437 time to fit residues: 1.7765 Evaluate side-chains 31 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.195576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110996 restraints weight = 3824.406| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.57 r_work: 0.2991 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3807 Z= 0.122 Angle : 0.412 5.494 5138 Z= 0.217 Chirality : 0.039 0.120 527 Planarity : 0.003 0.030 640 Dihedral : 10.081 58.540 610 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.08 % Allowed : 15.63 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.17 (0.40), residues: 450 helix: 2.45 (0.39), residues: 172 sheet: 1.02 (0.44), residues: 118 loop : 0.78 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.011 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 3805) covalent geometry : angle 0.41144 / 0.22 ( 5134) SS BOND : bond 0.00097 / 0.06 ( 2) SS BOND : angle 0.50767 / 0.24 ( 4) hydrogen bonds : bond 0.03133 / 2.23 ( 210) hydrogen bonds : angle 3.83181 / 2.76 ( 582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8585 (m-40) cc_final: 0.8347 (m110) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.0666 time to fit residues: 2.8992 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.196246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112162 restraints weight = 3700.911| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.54 r_work: 0.3008 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3807 Z= 0.110 Angle : 0.402 5.465 5138 Z= 0.212 Chirality : 0.039 0.120 527 Planarity : 0.003 0.030 640 Dihedral : 9.995 58.548 610 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.62 % Allowed : 15.36 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.23 (0.40), residues: 450 helix: 2.51 (0.39), residues: 172 sheet: 1.03 (0.44), residues: 118 loop : 0.82 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.010 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 3805) covalent geometry : angle 0.40242 / 0.21 ( 5134) SS BOND : bond 0.00106 / 0.06 ( 2) SS BOND : angle 0.46710 / 0.23 ( 4) hydrogen bonds : bond 0.03056 / 2.17 ( 210) hydrogen bonds : angle 3.77072 / 2.71 ( 582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.12 seconds wall clock time: 25 minutes 38.92 seconds (1538.92 seconds total)