Starting phenix.real_space_refine on Fri Aug 22 12:56:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j28_35947/08_2025/8j28_35947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j28_35947/08_2025/8j28_35947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j28_35947/08_2025/8j28_35947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j28_35947/08_2025/8j28_35947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j28_35947/08_2025/8j28_35947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j28_35947/08_2025/8j28_35947.map" } resolution = 3.7 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 9 5.16 5 C 1572 2.51 5 N 441 2.21 5 O 474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2499 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 147 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "C" Number of atoms: 2047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2048 Chain: "E" Number of atoms: 140 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Conformer: "B" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} bond proxies already assigned to first conformer: 115 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR C 72 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 72 " occ=0.50 residue: pdb=" N ATYR E 72 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 72 " occ=0.50 Time building chain proxies: 1.44, per 1000 atoms: 0.58 Number of scatterers: 2499 At special positions: 0 Unit cell: (74.2, 68.9, 78.44, 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 9 16.00 P 3 15.00 O 474 8.00 N 441 7.00 C 1572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 179.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP C 802 " Number of C-beta restraints generated: 584 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 56.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'F' and resid 72 through 77 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.624A pdb=" N LYS C 12 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 removed outlier: 3.601A pdb=" N GLY C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 77 removed outlier: 3.553A pdb=" N LEU C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 91 through 114 removed outlier: 4.226A pdb=" N SER C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.898A pdb=" N PHE C 128 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.813A pdb=" N LYS C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 238 through 251 removed outlier: 4.193A pdb=" N LYS C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 Processing helix chain 'E' and resid 72 through 78 Processing helix chain 'E' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'C' and resid 118 through 123 removed outlier: 3.670A pdb=" N ALA C 119 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 152 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 121 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN C 154 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 123 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL C 55 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N PHE C 153 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 57 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLU C 155 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER C 59 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 191 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 257 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 256 " --> pdb=" O PHE C 280 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 343 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: 0.38 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 409 1.31 - 1.44: 662 1.44 - 1.56: 1444 1.56 - 1.69: 4 1.69 - 1.82: 16 Bond restraints: 2535 Sorted by residual: bond pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " ideal model delta sigma weight residual 1.798 1.648 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD RGP C 802 " pdb=" OE2 RGP C 802 " ideal model delta sigma weight residual 1.302 1.397 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" N ARG C 67 " pdb=" CA ARG C 67 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA LEU C 65 " pdb=" C LEU C 65 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.36e-02 5.41e+03 8.67e+00 bond pdb=" CA LEU E 83 " pdb=" C LEU E 83 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.39e-02 5.18e+03 6.34e+00 ... (remaining 2530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 3315 2.36 - 4.72: 81 4.72 - 7.09: 17 7.09 - 9.45: 5 9.45 - 11.81: 1 Bond angle restraints: 3419 Sorted by residual: angle pdb=" N LEU C 65 " pdb=" CA LEU C 65 " pdb=" C LEU C 65 " ideal model delta sigma weight residual 111.71 103.48 8.23 1.15e+00 7.56e-01 5.12e+01 angle pdb=" N LEU E 83 " pdb=" CA LEU E 83 " pdb=" C LEU E 83 " ideal model delta sigma weight residual 111.75 103.06 8.69 1.28e+00 6.10e-01 4.61e+01 angle pdb=" N VAL C 25 " pdb=" CA VAL C 25 " pdb=" C VAL C 25 " ideal model delta sigma weight residual 113.42 108.56 4.86 1.17e+00 7.31e-01 1.72e+01 angle pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " pdb=" OA3 RGP C 802 " ideal model delta sigma weight residual 97.78 109.59 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N ARG C 67 " pdb=" CA ARG C 67 " pdb=" C ARG C 67 " ideal model delta sigma weight residual 111.11 106.67 4.44 1.20e+00 6.94e-01 1.37e+01 ... (remaining 3414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.27: 1458 33.27 - 66.54: 60 66.54 - 99.80: 5 99.80 - 133.07: 1 133.07 - 166.33: 1 Dihedral angle restraints: 1525 sinusoidal: 618 harmonic: 907 Sorted by residual: dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 106.33 -166.33 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP C 801 " pdb=" O5' ADP C 801 " pdb=" PA ADP C 801 " pdb=" O2A ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 40.34 -100.34 1 2.00e+01 2.50e-03 2.83e+01 dihedral pdb=" CA GLU C 220 " pdb=" C GLU C 220 " pdb=" N LYS C 221 " pdb=" CA LYS C 221 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 231 0.031 - 0.061: 103 0.061 - 0.092: 29 0.092 - 0.122: 22 0.122 - 0.153: 5 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA GLN C 68 " pdb=" N GLN C 68 " pdb=" C GLN C 68 " pdb=" CB GLN C 68 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE C 56 " pdb=" N ILE C 56 " pdb=" C ILE C 56 " pdb=" CB ILE C 56 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE C 150 " pdb=" N ILE C 150 " pdb=" C ILE C 150 " pdb=" CB ILE C 150 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 387 not shown) Planarity restraints: 431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BTYR C 72 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C BTYR C 72 " 0.067 2.00e-02 2.50e+03 pdb=" O BTYR C 72 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG C 73 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 71 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ARG C 71 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG C 71 " 0.023 2.00e-02 2.50e+03 pdb=" N ATYR C 72 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATYR C 72 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C ATYR C 72 " 0.062 2.00e-02 2.50e+03 pdb=" O ATYR C 72 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG C 73 " -0.021 2.00e-02 2.50e+03 ... (remaining 428 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 368 2.75 - 3.29: 2499 3.29 - 3.83: 3975 3.83 - 4.36: 4469 4.36 - 4.90: 7524 Nonbonded interactions: 18835 Sorted by model distance: nonbonded pdb=" OE2 GLU C 199 " pdb=" OH TYR C 202 " model vdw 2.213 3.040 nonbonded pdb=" OG SER C 60 " pdb=" OD1 ASN C 176 " model vdw 2.223 3.040 nonbonded pdb=" N GLU C 199 " pdb=" OE1 GLU C 199 " model vdw 2.252 3.120 nonbonded pdb=" O THR C 161 " pdb=" OG1 THR C 161 " model vdw 2.295 3.040 nonbonded pdb=" O SER F 79 " pdb=" N ASP F 82 " model vdw 2.345 3.120 ... (remaining 18830 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 71 or resid 73 through 85)) selection = (chain 'E' and (resid 71 or resid 73 through 85)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.020 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.006 0.150 2535 Z= 0.389 Angle : 0.923 11.812 3419 Z= 0.531 Chirality : 0.044 0.153 390 Planarity : 0.005 0.039 431 Dihedral : 17.631 166.335 941 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.28 % Allowed : 21.29 % Favored : 76.43 % 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 aren not related in a simple way. whole: -1.56 (0.46), residues: 307 helix: -0.70 (0.38), residues: 166 sheet: -0.37 (0.84), residues: 42 loop : -1.65 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 134 TYR 0.007 0.001 TYR A 72 PHE 0.015 0.001 PHE C 128 TRP 0.002 0.001 TRP C 287 HIS 0.005 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 2535) covalent geometry : angle 0.92339 ( 3419) hydrogen bonds : bond 0.18396 ( 119) hydrogen bonds : angle 7.70046 ( 343) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: F 75 LEU cc_start: 0.9313 (mm) cc_final: 0.9105 (mp) REVERT: F 82 ASP cc_start: 0.9501 (m-30) cc_final: 0.9277 (m-30) REVERT: A 73 ARG cc_start: 0.9110 (tpt90) cc_final: 0.8074 (ttp-170) REVERT: C 47 GLU cc_start: 0.8001 (pp20) cc_final: 0.7759 (pp20) REVERT: C 73 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8136 (tmt170) REVERT: C 100 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 154 ASN cc_start: 0.8312 (t0) cc_final: 0.8109 (t0) REVERT: C 198 VAL cc_start: 0.8813 (m) cc_final: 0.8598 (p) REVERT: C 208 ASP cc_start: 0.7813 (p0) cc_final: 0.7601 (p0) outliers start: 6 outliers final: 2 residues processed: 122 average time/residue: 0.0589 time to fit residues: 8.0531 Evaluate side-chains 87 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 223 GLN C 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.098555 restraints weight = 29991.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103469 restraints weight = 8082.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106750 restraints weight = 3991.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108921 restraints weight = 2476.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110482 restraints weight = 1759.703| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2535 Z= 0.144 Angle : 0.715 5.745 3419 Z= 0.353 Chirality : 0.041 0.145 390 Planarity : 0.005 0.042 431 Dihedral : 12.125 146.212 367 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.18 % Allowed : 31.18 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.48), residues: 307 helix: 0.41 (0.40), residues: 166 sheet: -0.46 (0.80), residues: 46 loop : -1.47 (0.63), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 129 TYR 0.015 0.001 TYR F 72 PHE 0.021 0.002 PHE F 80 TRP 0.003 0.001 TRP C 174 HIS 0.007 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2535) covalent geometry : angle 0.71481 ( 3419) hydrogen bonds : bond 0.03863 ( 119) hydrogen bonds : angle 5.20648 ( 343) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8879 (tpt90) cc_final: 0.7971 (ttt180) REVERT: C 12 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8456 (pttt) REVERT: C 47 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8767 (pp20) REVERT: C 73 ARG cc_start: 0.8760 (mmm160) cc_final: 0.7732 (tmt170) REVERT: C 100 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 154 ASN cc_start: 0.8709 (t0) cc_final: 0.8390 (t0) REVERT: C 198 VAL cc_start: 0.9326 (m) cc_final: 0.9104 (p) REVERT: C 199 GLU cc_start: 0.8925 (pm20) cc_final: 0.8646 (pm20) REVERT: C 208 ASP cc_start: 0.7017 (p0) cc_final: 0.6793 (p0) REVERT: C 239 MET cc_start: 0.8356 (mtp) cc_final: 0.8135 (mtp) REVERT: E 73 ARG cc_start: 0.7761 (ptp90) cc_final: 0.7523 (ptt-90) outliers start: 11 outliers final: 5 residues processed: 100 average time/residue: 0.0717 time to fit residues: 8.0818 Evaluate side-chains 94 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 161 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097951 restraints weight = 32270.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102971 restraints weight = 8269.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106293 restraints weight = 4030.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108571 restraints weight = 2483.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110072 restraints weight = 1745.535| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2535 Z= 0.132 Angle : 0.731 9.663 3419 Z= 0.343 Chirality : 0.042 0.138 390 Planarity : 0.004 0.032 431 Dihedral : 10.865 123.490 365 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.32 % Allowed : 29.66 % Favored : 65.02 % 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 aren not related in a simple way. whole: -0.36 (0.48), residues: 307 helix: 0.49 (0.40), residues: 166 sheet: -0.40 (0.81), residues: 46 loop : -1.29 (0.64), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 129 TYR 0.003 0.001 TYR C 202 PHE 0.014 0.002 PHE A 80 TRP 0.006 0.001 TRP C 174 HIS 0.005 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2535) covalent geometry : angle 0.73059 ( 3419) hydrogen bonds : bond 0.03528 ( 119) hydrogen bonds : angle 4.85443 ( 343) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8885 (tpt90) cc_final: 0.7951 (ttt180) REVERT: A 80 PHE cc_start: 0.9136 (t80) cc_final: 0.8859 (t80) REVERT: C 47 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8810 (pp20) REVERT: C 73 ARG cc_start: 0.8797 (mmm160) cc_final: 0.7608 (tmt170) REVERT: C 88 MET cc_start: 0.8262 (mmp) cc_final: 0.7987 (tpp) REVERT: C 100 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8189 (tm-30) REVERT: C 154 ASN cc_start: 0.8715 (t0) cc_final: 0.8391 (t0) REVERT: C 198 VAL cc_start: 0.9352 (m) cc_final: 0.9122 (p) REVERT: C 199 GLU cc_start: 0.8935 (pm20) cc_final: 0.8706 (pm20) REVERT: C 208 ASP cc_start: 0.7021 (p0) cc_final: 0.6783 (p0) REVERT: C 219 LYS cc_start: 0.9184 (mmtp) cc_final: 0.8964 (mmtp) REVERT: C 239 MET cc_start: 0.8455 (mtp) cc_final: 0.8168 (mtp) REVERT: E 73 ARG cc_start: 0.7768 (ptp90) cc_final: 0.7532 (ptt-90) outliers start: 14 outliers final: 5 residues processed: 98 average time/residue: 0.0868 time to fit residues: 9.6185 Evaluate side-chains 96 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.119585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096038 restraints weight = 26683.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100667 restraints weight = 7589.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103732 restraints weight = 3856.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105885 restraints weight = 2432.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107317 restraints weight = 1729.257| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2535 Z= 0.171 Angle : 0.722 6.902 3419 Z= 0.349 Chirality : 0.043 0.177 390 Planarity : 0.004 0.026 431 Dihedral : 10.429 103.782 365 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.46 % Allowed : 29.66 % Favored : 63.88 % 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 aren not related in a simple way. whole: -0.26 (0.48), residues: 307 helix: 0.57 (0.41), residues: 166 sheet: -0.08 (1.03), residues: 30 loop : -1.24 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 129 TYR 0.003 0.001 TYR C 107 PHE 0.031 0.003 PHE C 80 TRP 0.004 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 2535) covalent geometry : angle 0.72171 ( 3419) hydrogen bonds : bond 0.03822 ( 119) hydrogen bonds : angle 4.87628 ( 343) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8953 (tpt90) cc_final: 0.7967 (ttt180) REVERT: C 12 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8291 (pttt) REVERT: C 42 CYS cc_start: 0.9018 (m) cc_final: 0.8522 (t) REVERT: C 47 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8819 (pp20) REVERT: C 73 ARG cc_start: 0.8853 (mmm160) cc_final: 0.7602 (tmt170) REVERT: C 93 LYS cc_start: 0.8347 (mttt) cc_final: 0.7577 (pttt) REVERT: C 100 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 154 ASN cc_start: 0.8802 (t0) cc_final: 0.8464 (t0) REVERT: C 198 VAL cc_start: 0.9410 (m) cc_final: 0.9180 (p) REVERT: C 199 GLU cc_start: 0.8951 (pm20) cc_final: 0.8712 (pm20) REVERT: C 208 ASP cc_start: 0.7192 (p0) cc_final: 0.6915 (p0) REVERT: C 239 MET cc_start: 0.8662 (mtp) cc_final: 0.8274 (mtp) REVERT: C 275 ARG cc_start: 0.5520 (mmt180) cc_final: 0.4283 (ttm170) REVERT: E 73 ARG cc_start: 0.7967 (ptp90) cc_final: 0.7426 (tmt170) REVERT: E 77 ASN cc_start: 0.9434 (m-40) cc_final: 0.8858 (m110) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.0734 time to fit residues: 7.9737 Evaluate side-chains 96 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097857 restraints weight = 24144.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102547 restraints weight = 7254.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105712 restraints weight = 3706.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107798 restraints weight = 2334.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109340 restraints weight = 1673.963| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2535 Z= 0.132 Angle : 0.754 12.720 3419 Z= 0.351 Chirality : 0.044 0.239 390 Planarity : 0.003 0.026 431 Dihedral : 9.901 93.307 365 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.08 % Allowed : 31.56 % Favored : 62.36 % 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 aren not related in a simple way. whole: -0.34 (0.48), residues: 307 helix: 0.47 (0.41), residues: 166 sheet: -0.09 (1.01), residues: 30 loop : -1.23 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.002 0.001 TYR A 72 PHE 0.012 0.002 PHE A 80 TRP 0.003 0.001 TRP C 174 HIS 0.005 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2535) covalent geometry : angle 0.75354 ( 3419) hydrogen bonds : bond 0.03407 ( 119) hydrogen bonds : angle 4.79242 ( 343) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8941 (tpt90) cc_final: 0.7973 (ttt180) REVERT: C 8 ARG cc_start: 0.8127 (mtt90) cc_final: 0.7904 (mpt180) REVERT: C 12 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8296 (mttt) REVERT: C 47 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8798 (pp20) REVERT: C 73 ARG cc_start: 0.8838 (mmm160) cc_final: 0.7546 (tmt170) REVERT: C 93 LYS cc_start: 0.8291 (mttt) cc_final: 0.7487 (pttt) REVERT: C 100 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8238 (tm-30) REVERT: C 154 ASN cc_start: 0.8760 (t0) cc_final: 0.8421 (t0) REVERT: C 198 VAL cc_start: 0.9349 (m) cc_final: 0.9084 (p) REVERT: C 208 ASP cc_start: 0.7172 (p0) cc_final: 0.6900 (p0) REVERT: C 239 MET cc_start: 0.8634 (mtp) cc_final: 0.8269 (mtp) REVERT: C 275 ARG cc_start: 0.5463 (mmt180) cc_final: 0.4279 (ttm170) outliers start: 16 outliers final: 8 residues processed: 97 average time/residue: 0.0863 time to fit residues: 9.4427 Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.0270 chunk 23 optimal weight: 0.0050 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 overall best weight: 1.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.096783 restraints weight = 32276.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101655 restraints weight = 8414.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104941 restraints weight = 4131.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107141 restraints weight = 2564.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108715 restraints weight = 1827.203| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2535 Z= 0.149 Angle : 0.741 11.214 3419 Z= 0.347 Chirality : 0.042 0.155 390 Planarity : 0.003 0.026 431 Dihedral : 9.690 89.046 365 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.32 % Allowed : 31.18 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.48), residues: 307 helix: 0.45 (0.41), residues: 166 sheet: -0.09 (1.00), residues: 30 loop : -1.27 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.006 0.001 TYR C 202 PHE 0.019 0.002 PHE A 80 TRP 0.003 0.001 TRP C 174 HIS 0.006 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2535) covalent geometry : angle 0.74123 ( 3419) hydrogen bonds : bond 0.03364 ( 119) hydrogen bonds : angle 4.70902 ( 343) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8958 (tpt90) cc_final: 0.8038 (ttt180) REVERT: C 8 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7923 (mpt180) REVERT: C 12 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8335 (mttt) REVERT: C 42 CYS cc_start: 0.8996 (m) cc_final: 0.8462 (t) REVERT: C 47 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8820 (pp20) REVERT: C 73 ARG cc_start: 0.8857 (mmm160) cc_final: 0.7545 (tmt170) REVERT: C 75 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8964 (tp) REVERT: C 93 LYS cc_start: 0.8322 (mttt) cc_final: 0.7517 (pttt) REVERT: C 100 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8212 (tm-30) REVERT: C 154 ASN cc_start: 0.8782 (t0) cc_final: 0.8445 (t0) REVERT: C 208 ASP cc_start: 0.7340 (p0) cc_final: 0.7023 (p0) REVERT: C 239 MET cc_start: 0.8671 (mtp) cc_final: 0.8288 (mtp) REVERT: C 275 ARG cc_start: 0.5518 (mmt180) cc_final: 0.4193 (ttm170) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.0877 time to fit residues: 9.2267 Evaluate side-chains 96 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097859 restraints weight = 30719.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102864 restraints weight = 8088.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106223 restraints weight = 3966.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108509 restraints weight = 2445.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110024 restraints weight = 1717.161| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2535 Z= 0.130 Angle : 0.761 10.918 3419 Z= 0.354 Chirality : 0.044 0.164 390 Planarity : 0.003 0.030 431 Dihedral : 9.514 84.382 365 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.70 % Allowed : 31.56 % Favored : 62.74 % 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 aren not related in a simple way. whole: -0.43 (0.48), residues: 307 helix: 0.44 (0.40), residues: 166 sheet: -0.91 (0.91), residues: 35 loop : -1.06 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.007 0.001 TYR A 72 PHE 0.009 0.001 PHE C 280 TRP 0.002 0.000 TRP C 174 HIS 0.004 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2535) covalent geometry : angle 0.76131 ( 3419) hydrogen bonds : bond 0.03215 ( 119) hydrogen bonds : angle 4.59768 ( 343) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8969 (tpt90) cc_final: 0.7965 (ttt180) REVERT: C 8 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7873 (mpt180) REVERT: C 12 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8429 (mttt) REVERT: C 17 ILE cc_start: 0.8366 (mt) cc_final: 0.7948 (tt) REVERT: C 47 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8798 (pp20) REVERT: C 75 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8974 (tp) REVERT: C 93 LYS cc_start: 0.8252 (mttt) cc_final: 0.7467 (pttt) REVERT: C 100 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8275 (tm-30) REVERT: C 154 ASN cc_start: 0.8748 (t0) cc_final: 0.8412 (t0) REVERT: C 179 LEU cc_start: 0.7862 (tt) cc_final: 0.7501 (tp) REVERT: C 208 ASP cc_start: 0.7269 (p0) cc_final: 0.6963 (p0) REVERT: C 239 MET cc_start: 0.8652 (mtp) cc_final: 0.8248 (mtp) REVERT: C 275 ARG cc_start: 0.5420 (mmt180) cc_final: 0.4029 (ttm170) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 0.0803 time to fit residues: 8.3503 Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.0040 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN C 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099515 restraints weight = 30738.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104578 restraints weight = 8081.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107957 restraints weight = 3961.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110257 restraints weight = 2448.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.111838 restraints weight = 1723.159| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2535 Z= 0.123 Angle : 0.768 10.461 3419 Z= 0.354 Chirality : 0.042 0.132 390 Planarity : 0.003 0.025 431 Dihedral : 9.423 86.362 365 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.80 % Allowed : 33.84 % Favored : 62.36 % 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 aren not related in a simple way. whole: -0.44 (0.49), residues: 307 helix: 0.44 (0.40), residues: 166 sheet: -0.92 (0.87), residues: 40 loop : -1.07 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.008 0.001 TYR C 106 PHE 0.019 0.002 PHE F 80 TRP 0.002 0.000 TRP C 174 HIS 0.004 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 2535) covalent geometry : angle 0.76818 ( 3419) hydrogen bonds : bond 0.03043 ( 119) hydrogen bonds : angle 4.55628 ( 343) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8947 (tpt90) cc_final: 0.7999 (ttt180) REVERT: C 12 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8461 (mttt) REVERT: C 17 ILE cc_start: 0.8388 (mt) cc_final: 0.7998 (tt) REVERT: C 47 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8781 (pp20) REVERT: C 75 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8933 (tp) REVERT: C 93 LYS cc_start: 0.8090 (mttt) cc_final: 0.7354 (pttm) REVERT: C 100 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 154 ASN cc_start: 0.8736 (t0) cc_final: 0.8408 (t0) REVERT: C 179 LEU cc_start: 0.7757 (tt) cc_final: 0.7317 (tp) REVERT: C 199 GLU cc_start: 0.8879 (pm20) cc_final: 0.8675 (pm20) REVERT: C 208 ASP cc_start: 0.7377 (p0) cc_final: 0.7057 (p0) REVERT: C 239 MET cc_start: 0.8632 (mtp) cc_final: 0.8194 (mtp) REVERT: C 275 ARG cc_start: 0.5400 (mmt180) cc_final: 0.4017 (ttm170) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.0840 time to fit residues: 8.7591 Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.099343 restraints weight = 35274.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104593 restraints weight = 8246.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.108138 restraints weight = 3924.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110521 restraints weight = 2393.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111964 restraints weight = 1666.645| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2535 Z= 0.134 Angle : 0.788 10.266 3419 Z= 0.368 Chirality : 0.044 0.134 390 Planarity : 0.003 0.024 431 Dihedral : 9.235 88.266 365 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.18 % Allowed : 34.60 % Favored : 61.22 % 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 aren not related in a simple way. whole: -0.51 (0.48), residues: 307 helix: 0.28 (0.40), residues: 172 sheet: -1.07 (0.88), residues: 35 loop : -0.94 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.008 0.001 TYR C 251 PHE 0.011 0.002 PHE C 217 TRP 0.003 0.001 TRP C 174 HIS 0.008 0.002 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2535) covalent geometry : angle 0.78769 ( 3419) hydrogen bonds : bond 0.03194 ( 119) hydrogen bonds : angle 4.55386 ( 343) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.114 Fit side-chains REVERT: A 73 ARG cc_start: 0.8951 (tpt90) cc_final: 0.7991 (ttt180) REVERT: C 47 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8787 (pp20) REVERT: C 75 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8945 (tp) REVERT: C 93 LYS cc_start: 0.7942 (mttt) cc_final: 0.7272 (pttt) REVERT: C 100 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 154 ASN cc_start: 0.8667 (t0) cc_final: 0.8357 (t0) REVERT: C 179 LEU cc_start: 0.7730 (tt) cc_final: 0.7257 (tp) REVERT: C 199 GLU cc_start: 0.8929 (pm20) cc_final: 0.8693 (pm20) REVERT: C 208 ASP cc_start: 0.7286 (p0) cc_final: 0.6981 (p0) REVERT: C 239 MET cc_start: 0.8638 (mtp) cc_final: 0.8239 (mtp) REVERT: C 275 ARG cc_start: 0.5282 (mmt180) cc_final: 0.3879 (ttm170) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.0797 time to fit residues: 8.2473 Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.0020 chunk 10 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN C 248 ASN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.100312 restraints weight = 28654.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105463 restraints weight = 7844.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108868 restraints weight = 3863.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111169 restraints weight = 2389.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112771 restraints weight = 1683.875| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2535 Z= 0.129 Angle : 0.807 10.076 3419 Z= 0.375 Chirality : 0.043 0.142 390 Planarity : 0.003 0.024 431 Dihedral : 8.751 90.674 363 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.80 % Allowed : 36.50 % Favored : 59.70 % 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 aren not related in a simple way. whole: -0.47 (0.49), residues: 307 helix: 0.28 (0.41), residues: 172 sheet: -1.10 (0.88), residues: 35 loop : -0.82 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.010 0.001 TYR C 251 PHE 0.020 0.002 PHE F 80 TRP 0.002 0.001 TRP C 174 HIS 0.006 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2535) covalent geometry : angle 0.80702 ( 3419) hydrogen bonds : bond 0.03361 ( 119) hydrogen bonds : angle 4.58011 ( 343) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8924 (tpt90) cc_final: 0.8054 (ttt180) REVERT: C 12 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8311 (pttt) REVERT: C 47 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8769 (pp20) REVERT: C 75 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8929 (tp) REVERT: C 93 LYS cc_start: 0.7969 (mttt) cc_final: 0.7309 (pttt) REVERT: C 100 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8362 (tm-30) REVERT: C 154 ASN cc_start: 0.8656 (t0) cc_final: 0.8340 (t0) REVERT: C 199 GLU cc_start: 0.8866 (pm20) cc_final: 0.8641 (pm20) REVERT: C 208 ASP cc_start: 0.7465 (p0) cc_final: 0.7159 (p0) REVERT: C 219 LYS cc_start: 0.9359 (mttt) cc_final: 0.9098 (mptt) REVERT: C 239 MET cc_start: 0.8612 (mtp) cc_final: 0.8235 (mtp) REVERT: C 275 ARG cc_start: 0.5243 (mmt180) cc_final: 0.3858 (ttm170) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.0816 time to fit residues: 8.2286 Evaluate side-chains 92 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN C 248 ASN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.124058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098929 restraints weight = 30805.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.104175 restraints weight = 8116.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.107623 restraints weight = 3954.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109936 restraints weight = 2452.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.111529 restraints weight = 1731.665| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2535 Z= 0.151 Angle : 0.853 11.798 3419 Z= 0.410 Chirality : 0.043 0.138 390 Planarity : 0.003 0.024 431 Dihedral : 8.718 92.870 363 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.80 % Allowed : 37.26 % Favored : 58.94 % 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 aren not related in a simple way. whole: -0.43 (0.49), residues: 307 helix: 0.32 (0.41), residues: 172 sheet: -1.07 (0.90), residues: 35 loop : -0.84 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.011 0.001 TYR C 251 PHE 0.011 0.002 PHE F 80 TRP 0.003 0.001 TRP C 174 HIS 0.006 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2535) covalent geometry : angle 0.85299 ( 3419) hydrogen bonds : bond 0.03490 ( 119) hydrogen bonds : angle 4.76798 ( 343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 744.80 seconds wall clock time: 13 minutes 30.78 seconds (810.78 seconds total)