Starting phenix.real_space_refine on Tue Aug 4 12:03:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wa1_65796/08_2026/9wa1_65796.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wa1_65796/08_2026/9wa1_65796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wa1_65796/08_2026/9wa1_65796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wa1_65796/08_2026/9wa1_65796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wa1_65796/08_2026/9wa1_65796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wa1_65796/08_2026/9wa1_65796.map" } resolution = 2.28 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1383 2.51 5 N 351 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2139 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 713 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.53, per 1000 atoms: 0.25 Number of scatterers: 2139 At special positions: 0 Unit cell: (78.12, 77.19, 32.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 402 8.00 N 351 7.00 C 1383 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: 0.15 Conformation dependent library (CDL) restraints added in 80.0 milliseconds 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 49.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 16 removed outlier: 6.790A pdb=" N LEU A 12 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LYS C 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.401A pdb=" N ALA A 19 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 32 removed outlier: 6.380A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL B 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN A 27 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL B 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 29 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS A 31 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.393A pdb=" N THR A 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU C 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU A 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.912A pdb=" N GLU A 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 67 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N VAL A 65 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ILE C 68 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 67 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 73 removed outlier: 6.265A pdb=" N GLU A 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.972A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N LYS A 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N TRP C 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 99 removed outlier: 6.622A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN B 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 110 removed outlier: 9.241A pdb=" N ARG A 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N ILE B 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ALA B 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALA A 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG C 104 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TYR A 105 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR C 106 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 107 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 108 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.737A pdb=" N TYR A 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.676A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 108 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: 0.17 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 672 1.34 - 1.46: 347 1.46 - 1.57: 1165 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 2190 Sorted by residual: bond pdb=" CB ASP B 18 " pdb=" CG ASP B 18 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" CB ASP C 18 " pdb=" CG ASP C 18 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" CB ASP A 18 " pdb=" CG ASP A 18 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" SD MET A 13 " pdb=" CE MET A 13 " ideal model delta sigma weight residual 1.791 1.771 0.020 2.50e-02 1.60e+03 6.31e-01 bond pdb=" N LYS C 15 " pdb=" CA LYS C 15 " ideal model delta sigma weight residual 1.462 1.453 0.010 1.20e-02 6.94e+03 6.27e-01 ... (remaining 2185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 2669 1.04 - 2.08: 247 2.08 - 3.13: 47 3.13 - 4.17: 16 4.17 - 5.21: 6 Bond angle restraints: 2985 Sorted by residual: angle pdb=" N SER B 100 " pdb=" CA SER B 100 " pdb=" C SER B 100 " ideal model delta sigma weight residual 108.23 111.38 -3.15 1.38e+00 5.25e-01 5.19e+00 angle pdb=" N SER A 100 " pdb=" CA SER A 100 " pdb=" C SER A 100 " ideal model delta sigma weight residual 108.23 111.37 -3.14 1.38e+00 5.25e-01 5.17e+00 angle pdb=" CB ARG A 34 " pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " ideal model delta sigma weight residual 111.30 116.51 -5.21 2.30e+00 1.89e-01 5.13e+00 angle pdb=" N SER C 100 " pdb=" CA SER C 100 " pdb=" C SER C 100 " ideal model delta sigma weight residual 108.23 111.35 -3.12 1.38e+00 5.25e-01 5.12e+00 angle pdb=" CB ARG B 34 " pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " ideal model delta sigma weight residual 111.30 116.48 -5.18 2.30e+00 1.89e-01 5.08e+00 ... (remaining 2980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 1130 14.26 - 28.52: 94 28.52 - 42.78: 33 42.78 - 57.04: 24 57.04 - 71.30: 9 Dihedral angle restraints: 1290 sinusoidal: 486 harmonic: 804 Sorted by residual: dihedral pdb=" CA PHE B 87 " pdb=" C PHE B 87 " pdb=" N HIS B 88 " pdb=" CA HIS B 88 " ideal model delta harmonic sigma weight residual 180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PHE A 87 " pdb=" C PHE A 87 " pdb=" N HIS A 88 " pdb=" CA HIS A 88 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PHE C 87 " pdb=" C PHE C 87 " pdb=" N HIS C 88 " pdb=" CA HIS C 88 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 189 0.025 - 0.049: 65 0.049 - 0.074: 44 0.074 - 0.098: 16 0.098 - 0.123: 40 Chirality restraints: 354 Sorted by residual: chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL B 65 " pdb=" N VAL B 65 " pdb=" C VAL B 65 " pdb=" CB VAL B 65 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 351 not shown) Planarity restraints: 369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " -0.010 2.00e-02 2.50e+03 7.93e-03 1.26e+00 pdb=" CG TYR C 114 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 114 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 114 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 114 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 114 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 35 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" CG ASN C 35 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 35 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 35 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " -0.009 2.00e-02 2.50e+03 7.89e-03 1.25e+00 pdb=" CG TYR A 114 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.001 2.00e-02 2.50e+03 ... (remaining 366 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 783 2.89 - 3.39: 1678 3.39 - 3.90: 3718 3.90 - 4.40: 3922 4.40 - 4.90: 7239 Nonbonded interactions: 17340 Sorted by model distance: nonbonded pdb=" NZ LYS A 70 " pdb=" OE2 GLU A 72 " model vdw 2.388 3.120 nonbonded pdb=" NZ LYS B 70 " pdb=" OE2 GLU B 72 " model vdw 2.389 3.120 nonbonded pdb=" NZ LYS C 70 " pdb=" OE2 GLU C 72 " model vdw 2.389 3.120 nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR C 119 " model vdw 2.435 3.040 nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR B 114 " model vdw 2.466 3.040 ... (remaining 17335 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.030 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:5.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2190 Z= 0.168 Angle : 0.711 5.209 2985 Z= 0.403 Chirality : 0.049 0.123 354 Planarity : 0.004 0.023 369 Dihedral : 16.202 71.302 768 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 19.23 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.45), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 21 TYR 0.019 0.002 TYR C 114 PHE 0.018 0.003 PHE B 33 TRP 0.004 0.001 TRP B 79 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 2190) covalent geometry : angle 0.71059 / 0.40 ( 2985) hydrogen bonds : bond 0.15968 / 11.52 ( 36) hydrogen bonds : angle 10.03419 / 6.97 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.049 Fit side-chains REVERT: A 80 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8539 (tttt) REVERT: A 104 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8291 (mtm-85) REVERT: B 104 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8409 (mtt-85) REVERT: C 80 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8682 (tttt) REVERT: C 104 ARG cc_start: 0.8851 (mtm-85) cc_final: 0.8535 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.4266 time to fit residues: 31.2119 Evaluate side-chains 64 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.0570 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN ** 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 = 0.4019 r_free = 0.4019 target = 0.140531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.120317 restraints weight = 2295.680| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.82 r_work: 0.3650 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2190 Z= 0.145 Angle : 0.550 4.240 2985 Z= 0.311 Chirality : 0.050 0.137 354 Planarity : 0.003 0.018 369 Dihedral : 5.736 19.836 294 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.42 % Allowed : 21.79 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.48), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 21 TYR 0.016 0.002 TYR B 114 PHE 0.013 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.002 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 2190) covalent geometry : angle 0.55042 / 0.31 ( 2985) hydrogen bonds : bond 0.03361 / 2.63 ( 36) hydrogen bonds : angle 6.70869 / 4.47 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.050 Fit side-chains REVERT: A 80 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8631 (tttt) REVERT: A 104 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8309 (mtm-85) REVERT: B 13 MET cc_start: 0.8432 (tmt) cc_final: 0.8140 (tmt) REVERT: B 61 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: B 104 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8310 (mtt-85) REVERT: C 13 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8405 (tmt) REVERT: C 15 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8198 (tmtt) REVERT: C 92 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: C 104 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8571 (mtm-85) outliers start: 8 outliers final: 0 residues processed: 64 average time/residue: 0.4825 time to fit residues: 31.3401 Evaluate side-chains 66 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.139991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.119785 restraints weight = 2322.306| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.83 r_work: 0.3646 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2190 Z= 0.143 Angle : 0.540 3.688 2985 Z= 0.306 Chirality : 0.050 0.134 354 Planarity : 0.003 0.018 369 Dihedral : 5.669 20.666 294 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.27 % Allowed : 20.94 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.49), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 21 TYR 0.014 0.002 TYR B 114 PHE 0.008 0.001 PHE A 95 TRP 0.003 0.001 TRP B 79 HIS 0.002 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 2190) covalent geometry : angle 0.53984 / 0.31 ( 2985) hydrogen bonds : bond 0.02916 / 2.27 ( 36) hydrogen bonds : angle 6.13434 / 4.05 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.050 Fit side-chains REVERT: A 34 ARG cc_start: 0.7109 (ttt180) cc_final: 0.6855 (tmm160) REVERT: A 80 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8672 (tttt) REVERT: A 104 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8307 (mtm-85) REVERT: B 13 MET cc_start: 0.8510 (tmt) cc_final: 0.8305 (tmt) REVERT: B 61 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7801 (pt0) REVERT: B 104 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8297 (mtt-85) REVERT: C 13 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8420 (tmt) REVERT: C 15 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8138 (tmtt) REVERT: C 92 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: C 104 ARG cc_start: 0.8776 (mtm-85) cc_final: 0.8558 (mtm-85) outliers start: 10 outliers final: 1 residues processed: 67 average time/residue: 0.6167 time to fit residues: 41.9329 Evaluate side-chains 68 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 92 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** 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 = 0.3994 r_free = 0.3994 target = 0.138257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.117726 restraints weight = 2312.958| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.82 r_work: 0.3620 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2190 Z= 0.183 Angle : 0.574 3.779 2985 Z= 0.326 Chirality : 0.050 0.134 354 Planarity : 0.003 0.019 369 Dihedral : 5.849 21.189 294 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.85 % Allowed : 22.22 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.48), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 103 TYR 0.014 0.002 TYR B 114 PHE 0.014 0.002 PHE A 33 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 ( 2190) covalent geometry : angle 0.57443 / 0.33 ( 2985) hydrogen bonds : bond 0.02925 / 2.27 ( 36) hydrogen bonds : angle 6.16103 / 4.11 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.097 Fit side-chains REVERT: B 13 MET cc_start: 0.8502 (tmt) cc_final: 0.8221 (tpp) REVERT: B 61 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: B 104 ARG cc_start: 0.8834 (mtm-85) cc_final: 0.8397 (mtt-85) REVERT: C 13 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8269 (tmt) REVERT: C 15 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8303 (tmtt) outliers start: 9 outliers final: 1 residues processed: 68 average time/residue: 0.7150 time to fit residues: 49.3244 Evaluate side-chains 70 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 15 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN ** 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 = 0.4037 r_free = 0.4037 target = 0.141863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.121887 restraints weight = 2308.920| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.79 r_work: 0.3675 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2190 Z= 0.122 Angle : 0.533 4.849 2985 Z= 0.298 Chirality : 0.049 0.132 354 Planarity : 0.003 0.017 369 Dihedral : 5.611 20.726 294 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.99 % Allowed : 23.08 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.48), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 21 TYR 0.014 0.002 TYR B 114 PHE 0.014 0.002 PHE B 33 TRP 0.002 0.001 TRP B 79 HIS 0.001 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 2190) covalent geometry : angle 0.53281 / 0.30 ( 2985) hydrogen bonds : bond 0.02563 / 1.99 ( 36) hydrogen bonds : angle 5.82330 / 3.87 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.049 Fit side-chains REVERT: A 13 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8137 (tmt) REVERT: A 34 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7312 (tmm160) REVERT: A 104 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8321 (mtm-85) REVERT: B 13 MET cc_start: 0.8517 (tmt) cc_final: 0.8252 (tpp) REVERT: B 104 ARG cc_start: 0.8822 (mtm-85) cc_final: 0.8371 (mtt-85) REVERT: C 13 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8180 (tmt) REVERT: C 15 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8346 (tttm) REVERT: C 66 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8148 (tp30) outliers start: 7 outliers final: 0 residues processed: 68 average time/residue: 0.6020 time to fit residues: 41.5566 Evaluate side-chains 69 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 15 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.138468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118356 restraints weight = 2281.205| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.79 r_work: 0.3634 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2190 Z= 0.165 Angle : 0.576 4.548 2985 Z= 0.323 Chirality : 0.050 0.133 354 Planarity : 0.003 0.019 369 Dihedral : 5.805 21.503 294 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.99 % Allowed : 23.08 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.48), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 21 TYR 0.013 0.002 TYR B 114 PHE 0.014 0.002 PHE A 33 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 2190) covalent geometry : angle 0.57597 / 0.32 ( 2985) hydrogen bonds : bond 0.02795 / 2.17 ( 36) hydrogen bonds : angle 5.96240 / 3.99 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.094 Fit side-chains REVERT: A 13 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8204 (tmt) REVERT: A 34 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7293 (tmm160) REVERT: B 13 MET cc_start: 0.8530 (tmt) cc_final: 0.8235 (tpp) REVERT: B 104 ARG cc_start: 0.8844 (mtm-85) cc_final: 0.8398 (mtt-85) REVERT: C 15 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8217 (tmtt) REVERT: C 18 ASP cc_start: 0.6651 (p0) cc_final: 0.6288 (p0) outliers start: 7 outliers final: 1 residues processed: 67 average time/residue: 0.6947 time to fit residues: 47.2662 Evaluate side-chains 69 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain C residue 15 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124113 restraints weight = 2247.272| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.81 r_work: 0.3723 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2190 Z= 0.098 Angle : 0.504 4.066 2985 Z= 0.280 Chirality : 0.049 0.129 354 Planarity : 0.003 0.016 369 Dihedral : 5.390 20.073 294 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.56 % Allowed : 23.50 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.48), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 21 TYR 0.012 0.001 TYR B 114 PHE 0.013 0.001 PHE B 33 TRP 0.001 0.000 TRP C 79 HIS 0.001 0.000 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 2190) covalent geometry : angle 0.50407 / 0.28 ( 2985) hydrogen bonds : bond 0.02375 / 1.83 ( 36) hydrogen bonds : angle 5.57336 / 3.70 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.104 Fit side-chains REVERT: A 13 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8212 (tmt) REVERT: A 34 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7345 (tmm160) REVERT: A 104 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8306 (mtm-85) REVERT: B 13 MET cc_start: 0.8531 (tmt) cc_final: 0.8106 (tpp) REVERT: B 104 ARG cc_start: 0.8807 (mtm-85) cc_final: 0.8347 (mtt-85) REVERT: C 15 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8267 (tmtt) REVERT: C 66 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8017 (tp30) outliers start: 6 outliers final: 0 residues processed: 66 average time/residue: 0.7022 time to fit residues: 47.0400 Evaluate side-chains 66 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain C residue 15 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.139826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.119782 restraints weight = 2298.058| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.79 r_work: 0.3656 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2190 Z= 0.141 Angle : 0.549 3.914 2985 Z= 0.308 Chirality : 0.049 0.131 354 Planarity : 0.003 0.018 369 Dihedral : 5.643 21.378 294 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.42 % Allowed : 22.22 % Favored : 74.36 % 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 are not related in a simple way. whole: -2.21 (0.49), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.013 0.002 TYR B 114 PHE 0.013 0.002 PHE A 33 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 2190) covalent geometry : angle 0.54852 / 0.31 ( 2985) hydrogen bonds : bond 0.02564 / 1.98 ( 36) hydrogen bonds : angle 5.71569 / 3.79 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.099 Fit side-chains REVERT: A 13 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8175 (tmt) REVERT: A 34 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7336 (tmm160) REVERT: A 104 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8305 (mtm-85) REVERT: B 61 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: B 104 ARG cc_start: 0.8834 (mtm-85) cc_final: 0.8370 (mtt-85) REVERT: C 15 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8361 (tmtt) REVERT: C 66 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8172 (tp30) outliers start: 8 outliers final: 1 residues processed: 66 average time/residue: 0.6349 time to fit residues: 42.5544 Evaluate side-chains 69 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 15 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.136454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116379 restraints weight = 2293.043| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.77 r_work: 0.3601 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2190 Z= 0.222 Angle : 0.621 3.929 2985 Z= 0.349 Chirality : 0.051 0.135 354 Planarity : 0.003 0.020 369 Dihedral : 6.005 21.885 294 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.99 % Allowed : 22.22 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.48), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 103 TYR 0.012 0.002 TYR B 114 PHE 0.014 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 ( 2190) covalent geometry : angle 0.62109 / 0.35 ( 2985) hydrogen bonds : bond 0.03029 / 2.32 ( 36) hydrogen bonds : angle 6.12131 / 4.09 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.084 Fit side-chains REVERT: A 13 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8156 (tmt) REVERT: B 104 ARG cc_start: 0.8851 (mtm-85) cc_final: 0.8387 (mtt-85) REVERT: C 15 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8496 (tttm) outliers start: 7 outliers final: 0 residues processed: 70 average time/residue: 0.5093 time to fit residues: 36.1899 Evaluate side-chains 70 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain C residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.142229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.121961 restraints weight = 2366.258| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.89 r_work: 0.3689 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2190 Z= 0.109 Angle : 0.552 6.474 2985 Z= 0.302 Chirality : 0.049 0.130 354 Planarity : 0.003 0.016 369 Dihedral : 5.578 20.369 294 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.14 % Allowed : 23.93 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.48), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 21 TYR 0.012 0.001 TYR A 114 PHE 0.013 0.001 PHE A 33 TRP 0.001 0.000 TRP B 79 HIS 0.001 0.000 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 2190) covalent geometry : angle 0.55179 / 0.30 ( 2985) hydrogen bonds : bond 0.02499 / 1.93 ( 36) hydrogen bonds : angle 5.61619 / 3.71 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.082 Fit side-chains REVERT: A 13 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8119 (tmt) REVERT: A 104 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8314 (mtm-85) REVERT: B 34 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7288 (tmm160) REVERT: B 104 ARG cc_start: 0.8832 (mtm-85) cc_final: 0.8335 (mtt-85) REVERT: C 13 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8414 (tmt) REVERT: C 15 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8314 (tmtt) REVERT: C 66 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8053 (tp30) outliers start: 5 outliers final: 0 residues processed: 65 average time/residue: 0.5565 time to fit residues: 36.7211 Evaluate side-chains 68 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.138686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118312 restraints weight = 2322.538| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.81 r_work: 0.3629 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2190 Z= 0.168 Angle : 0.603 6.439 2985 Z= 0.334 Chirality : 0.050 0.133 354 Planarity : 0.003 0.018 369 Dihedral : 5.812 21.561 294 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.56 % Allowed : 23.08 % Favored : 74.36 % 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 are not related in a simple way. whole: -2.22 (0.49), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 103 TYR 0.013 0.002 TYR B 114 PHE 0.015 0.002 PHE B 33 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 2190) covalent geometry : angle 0.60274 / 0.33 ( 2985) hydrogen bonds : bond 0.02734 / 2.10 ( 36) hydrogen bonds : angle 5.81335 / 3.87 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1194.78 seconds wall clock time: 21 minutes 1.39 seconds (1261.39 seconds total)