Starting phenix.real_space_refine on Tue Aug 4 12:03:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9u_65789/08_2026/9w9u_65789.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9u_65789/08_2026/9w9u_65789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9u_65789/08_2026/9w9u_65789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9u_65789/08_2026/9w9u_65789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9u_65789/08_2026/9w9u_65789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9u_65789/08_2026/9w9u_65789.map" } resolution = 2.35 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 1398 2.51 5 N 357 2.21 5 O 396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 2154 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.54, per 1000 atoms: 0.25 Number of scatterers: 2154 At special positions: 0 Unit cell: (72.54, 81.84, 31.62, 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 396 8.00 N 357 7.00 C 1398 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: 0.10 Conformation dependent library (CDL) restraints added in 56.5 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 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 9 sheets defined 0.0% alpha, 50.0% 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 13 through 16 removed outlier: 6.387A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.498A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 34 removed outlier: 6.322A pdb=" N ALA A 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN A 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL C 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA A 29 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL C 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ARG C 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 73 removed outlier: 9.122A pdb=" N THR A 60 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N GLU B 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU A 62 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N VAL B 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 64 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N GLY B 67 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N GLU A 66 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR B 69 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE A 68 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL B 71 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU A 72 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR C 60 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS A 61 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU C 62 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU A 63 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 68 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR A 69 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.454A pdb=" N TRP A 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 97 removed outlier: 6.433A pdb=" N GLU A 92 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE B 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 94 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALA B 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR A 96 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 110 removed outlier: 8.981A pdb=" N ARG A 103 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N THR B 106 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N ALA B 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 107 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU B 110 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA A 109 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG A 104 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR C 105 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE C 107 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA A 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.878A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.822A pdb=" N THR A 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL C 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) 35 hydrogen bonds defined for protein. 105 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: 0.19 Time building geometry restraints manager: 0.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 666 1.34 - 1.46: 323 1.46 - 1.57: 1210 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 2205 Sorted by residual: bond pdb=" CG1 ILE C 68 " pdb=" CD1 ILE C 68 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.11e+00 bond pdb=" CG1 ILE A 68 " pdb=" CD1 ILE A 68 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.11e+00 bond pdb=" CG1 ILE B 68 " pdb=" CD1 ILE B 68 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.05e+00 bond pdb=" CD LYS B 76 " pdb=" CE LYS B 76 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.36e-01 bond pdb=" CD LYS C 76 " pdb=" CE LYS C 76 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.07e-01 ... (remaining 2200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 2659 1.01 - 2.03: 250 2.03 - 3.04: 55 3.04 - 4.06: 21 4.06 - 5.07: 12 Bond angle restraints: 2997 Sorted by residual: angle pdb=" C GLU A 63 " pdb=" N PHE A 64 " pdb=" CA PHE A 64 " ideal model delta sigma weight residual 122.36 117.90 4.46 1.60e+00 3.91e-01 7.77e+00 angle pdb=" C GLU C 63 " pdb=" N PHE C 64 " pdb=" CA PHE C 64 " ideal model delta sigma weight residual 122.36 117.93 4.43 1.60e+00 3.91e-01 7.68e+00 angle pdb=" C GLU B 63 " pdb=" N PHE B 64 " pdb=" CA PHE B 64 " ideal model delta sigma weight residual 122.36 117.94 4.42 1.60e+00 3.91e-01 7.63e+00 angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 118.68 -4.78 1.80e+00 3.09e-01 7.06e+00 angle pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.99e+00 ... (remaining 2992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1203 17.88 - 35.76: 81 35.76 - 53.64: 15 53.64 - 71.51: 0 71.51 - 89.39: 3 Dihedral angle restraints: 1302 sinusoidal: 495 harmonic: 807 Sorted by residual: dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE A 26 " pdb=" C ILE A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE C 26 " pdb=" C ILE C 26 " pdb=" N ASN C 27 " pdb=" CA ASN C 27 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 1299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 223 0.048 - 0.096: 90 0.096 - 0.144: 38 0.144 - 0.192: 0 0.192 - 0.240: 3 Chirality restraints: 354 Sorted by residual: chirality pdb=" CB THR B 106 " pdb=" CA THR B 106 " pdb=" OG1 THR B 106 " pdb=" CG2 THR B 106 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB THR A 106 " pdb=" CA THR A 106 " pdb=" OG1 THR A 106 " pdb=" CG2 THR A 106 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB THR C 106 " pdb=" CA THR C 106 " pdb=" OG1 THR C 106 " pdb=" CG2 THR C 106 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 351 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " -0.011 2.00e-02 2.50e+03 9.09e-03 1.65e+00 pdb=" CG TYR A 114 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " -0.011 2.00e-02 2.50e+03 8.77e-03 1.54e+00 pdb=" CG TYR C 114 " 0.021 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 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " -0.000 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 TYR B 114 " -0.011 2.00e-02 2.50e+03 8.73e-03 1.53e+00 pdb=" CG TYR B 114 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " -0.001 2.00e-02 2.50e+03 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 644 2.86 - 3.37: 1677 3.37 - 3.88: 3757 3.88 - 4.39: 3883 4.39 - 4.90: 7594 Nonbonded interactions: 17555 Sorted by model distance: nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR C 114 " model vdw 2.345 3.040 nonbonded pdb=" OH TYR A 105 " pdb=" OD2 ASP B 74 " model vdw 2.368 3.040 nonbonded pdb=" OD2 ASP A 74 " pdb=" OH TYR C 105 " model vdw 2.371 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR B 119 " model vdw 2.402 3.040 nonbonded pdb=" O THR C 59 " pdb=" OG1 THR C 59 " model vdw 2.600 3.040 ... (remaining 17550 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' 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: 0.510 Set stop_for_unknowns flag: 0.010 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.810 Find NCS groups from input model: 0.010 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:5.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2205 Z= 0.196 Angle : 0.764 5.074 2997 Z= 0.445 Chirality : 0.058 0.240 354 Planarity : 0.004 0.019 366 Dihedral : 12.999 89.391 780 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: -2.77 (0.42), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.022 0.002 TYR A 114 PHE 0.014 0.003 PHE A 64 TRP 0.003 0.002 TRP C 79 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 ( 2205) covalent geometry : angle 0.76421 / 0.44 ( 2997) hydrogen bonds : bond 0.15282 / 8.39 ( 35) hydrogen bonds : angle 9.08620 / 5.84 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.055 Fit side-chains REVERT: A 13 MET cc_start: 0.8147 (ttm) cc_final: 0.7764 (ttt) REVERT: A 62 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7607 (tt0) REVERT: A 104 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8256 (mtt90) REVERT: B 13 MET cc_start: 0.8069 (ttm) cc_final: 0.7713 (ttm) REVERT: B 15 LYS cc_start: 0.8669 (mttt) cc_final: 0.8445 (mtpt) REVERT: B 62 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7613 (tt0) REVERT: B 104 ARG cc_start: 0.8819 (mtt180) cc_final: 0.8373 (mtt90) REVERT: C 62 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7763 (tt0) REVERT: C 63 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8137 (mt-10) REVERT: C 66 GLU cc_start: 0.8235 (tt0) cc_final: 0.7990 (tt0) REVERT: C 104 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8347 (mtt90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.5201 time to fit residues: 26.8911 Evaluate side-chains 50 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.095910 restraints weight = 2334.165| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.77 r_work: 0.3240 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 2205 Z= 0.284 Angle : 0.675 4.285 2997 Z= 0.390 Chirality : 0.057 0.136 354 Planarity : 0.004 0.027 366 Dihedral : 6.316 22.763 297 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.43 % Allowed : 10.26 % Favored : 89.32 % 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: -2.58 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 103 TYR 0.016 0.002 TYR B 114 PHE 0.016 0.003 PHE C 95 TRP 0.006 0.002 TRP A 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.28 ( 2205) covalent geometry : angle 0.67517 / 0.39 ( 2997) hydrogen bonds : bond 0.03727 / 2.17 ( 35) hydrogen bonds : angle 6.63999 / 4.34 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.051 Fit side-chains REVERT: A 13 MET cc_start: 0.8137 (ttm) cc_final: 0.7773 (ttt) REVERT: A 104 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8031 (mtt90) REVERT: B 15 LYS cc_start: 0.8678 (mttt) cc_final: 0.8446 (mtpt) REVERT: B 104 ARG cc_start: 0.8841 (mtt180) cc_final: 0.8322 (mtt90) REVERT: C 104 ARG cc_start: 0.8790 (mtt180) cc_final: 0.8514 (mtt90) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.5297 time to fit residues: 29.5351 Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.0370 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.121238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101385 restraints weight = 2327.040| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.76 r_work: 0.3328 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2205 Z= 0.119 Angle : 0.525 4.057 2997 Z= 0.302 Chirality : 0.050 0.130 354 Planarity : 0.003 0.023 366 Dihedral : 5.621 20.929 297 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.85 % Allowed : 13.25 % Favored : 85.90 % 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: -2.51 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 34 TYR 0.014 0.001 TYR A 114 PHE 0.011 0.002 PHE A 64 TRP 0.001 0.000 TRP C 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 2205) covalent geometry : angle 0.52478 / 0.30 ( 2997) hydrogen bonds : bond 0.02698 / 1.41 ( 35) hydrogen bonds : angle 6.01521 / 3.92 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.083 Fit side-chains REVERT: A 13 MET cc_start: 0.8101 (ttm) cc_final: 0.7748 (ttt) REVERT: A 104 ARG cc_start: 0.8658 (mtt180) cc_final: 0.8095 (mtt90) REVERT: B 15 LYS cc_start: 0.8670 (mttt) cc_final: 0.8444 (mtpt) REVERT: B 104 ARG cc_start: 0.8766 (mtt180) cc_final: 0.8308 (mtt90) REVERT: C 104 ARG cc_start: 0.8757 (mtt180) cc_final: 0.8478 (mtt90) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.6567 time to fit residues: 36.6051 Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.114902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094246 restraints weight = 2274.031| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.75 r_work: 0.3217 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 2205 Z= 0.342 Angle : 0.721 4.360 2997 Z= 0.416 Chirality : 0.059 0.166 354 Planarity : 0.005 0.030 366 Dihedral : 6.483 22.433 297 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.85 % Allowed : 15.38 % Favored : 83.76 % 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: -2.43 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 103 TYR 0.018 0.002 TYR B 114 PHE 0.017 0.003 PHE C 95 TRP 0.006 0.002 TRP A 79 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00822 / 0.34 ( 2205) covalent geometry : angle 0.72102 / 0.42 ( 2997) hydrogen bonds : bond 0.03530 / 1.98 ( 35) hydrogen bonds : angle 6.41576 / 4.18 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.083 Fit side-chains REVERT: A 13 MET cc_start: 0.8185 (ttm) cc_final: 0.7818 (ttt) REVERT: A 104 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8129 (mtt90) REVERT: B 15 LYS cc_start: 0.8695 (mttt) cc_final: 0.8446 (mtpt) REVERT: B 104 ARG cc_start: 0.8820 (mtt180) cc_final: 0.8287 (mtt90) REVERT: C 13 MET cc_start: 0.8525 (ttm) cc_final: 0.8263 (ttm) REVERT: C 104 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8480 (mtt90) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.8429 time to fit residues: 46.9545 Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 2.0064 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.120532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.100331 restraints weight = 2296.007| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.76 r_work: 0.3322 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2205 Z= 0.128 Angle : 0.549 3.933 2997 Z= 0.314 Chirality : 0.051 0.130 354 Planarity : 0.003 0.032 366 Dihedral : 5.817 21.363 297 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.43 % Allowed : 17.09 % Favored : 82.48 % 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: -2.45 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.016 0.002 TYR A 114 PHE 0.011 0.002 PHE A 64 TRP 0.001 0.001 TRP C 79 HIS 0.003 0.000 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 2205) covalent geometry : angle 0.54892 / 0.31 ( 2997) hydrogen bonds : bond 0.02574 / 1.35 ( 35) hydrogen bonds : angle 5.90987 / 3.83 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.084 Fit side-chains REVERT: A 13 MET cc_start: 0.8149 (ttm) cc_final: 0.7805 (ttt) REVERT: A 104 ARG cc_start: 0.8635 (mtt180) cc_final: 0.8116 (mtt90) REVERT: B 15 LYS cc_start: 0.8679 (mttt) cc_final: 0.8439 (mtpt) REVERT: B 104 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8313 (mtt90) REVERT: C 61 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8355 (mtmm) REVERT: C 104 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8475 (mtt90) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.7023 time to fit residues: 39.1720 Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 25 optimal weight: 0.0970 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.125945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.107672 restraints weight = 2293.107| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.66 r_work: 0.3456 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2205 Z= 0.084 Angle : 0.469 3.868 2997 Z= 0.266 Chirality : 0.049 0.126 354 Planarity : 0.003 0.026 366 Dihedral : 5.070 19.089 297 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.43 % Allowed : 17.95 % Favored : 81.62 % 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: -2.42 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.013 0.001 TYR C 114 PHE 0.011 0.002 PHE A 64 TRP 0.002 0.000 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.08 ( 2205) covalent geometry : angle 0.46860 / 0.27 ( 2997) hydrogen bonds : bond 0.02104 / 0.97 ( 35) hydrogen bonds : angle 5.60468 / 3.61 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.076 Fit side-chains REVERT: A 104 ARG cc_start: 0.8653 (mtt180) cc_final: 0.8145 (mtt90) REVERT: B 15 LYS cc_start: 0.8665 (mttt) cc_final: 0.8452 (mtpt) REVERT: B 104 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8268 (mtt90) REVERT: C 104 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8432 (mtt90) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.6494 time to fit residues: 32.9719 Evaluate side-chains 48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096785 restraints weight = 2269.637| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.74 r_work: 0.3258 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2205 Z= 0.247 Angle : 0.636 4.067 2997 Z= 0.367 Chirality : 0.054 0.136 354 Planarity : 0.004 0.037 366 Dihedral : 6.027 22.394 297 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.85 % Allowed : 18.80 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.017 0.002 TYR B 114 PHE 0.015 0.003 PHE C 95 TRP 0.005 0.001 TRP A 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 ( 2205) covalent geometry : angle 0.63630 / 0.37 ( 2997) hydrogen bonds : bond 0.03050 / 1.68 ( 35) hydrogen bonds : angle 6.01997 / 3.91 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.051 Fit side-chains REVERT: A 13 MET cc_start: 0.8122 (ttm) cc_final: 0.7772 (ttt) REVERT: A 104 ARG cc_start: 0.8628 (mtt180) cc_final: 0.8108 (mtt90) REVERT: B 15 LYS cc_start: 0.8645 (mttt) cc_final: 0.8407 (mtpt) REVERT: B 104 ARG cc_start: 0.8826 (mtt180) cc_final: 0.8342 (mtt90) REVERT: C 61 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8356 (mtmm) REVERT: C 104 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8488 (mtt90) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.8110 time to fit residues: 43.5814 Evaluate side-chains 54 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.122020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102114 restraints weight = 2272.242| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.74 r_work: 0.3355 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2205 Z= 0.103 Angle : 0.513 3.904 2997 Z= 0.293 Chirality : 0.049 0.129 354 Planarity : 0.003 0.031 366 Dihedral : 5.499 20.842 297 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.43 % Allowed : 19.23 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 34 TYR 0.014 0.001 TYR C 114 PHE 0.012 0.002 PHE A 64 TRP 0.001 0.000 TRP A 79 HIS 0.003 0.000 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.10 ( 2205) covalent geometry : angle 0.51276 / 0.29 ( 2997) hydrogen bonds : bond 0.02288 / 1.14 ( 35) hydrogen bonds : angle 5.68252 / 3.69 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.095 Fit side-chains REVERT: A 13 MET cc_start: 0.8071 (ttm) cc_final: 0.7735 (ttt) REVERT: A 104 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8099 (mtt90) REVERT: B 15 LYS cc_start: 0.8653 (mttt) cc_final: 0.8428 (mtpt) REVERT: B 104 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8283 (mtt90) REVERT: C 104 ARG cc_start: 0.8736 (mtt180) cc_final: 0.8463 (mtt90) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.8103 time to fit residues: 42.7260 Evaluate side-chains 52 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.0170 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.119155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.098604 restraints weight = 2279.229| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.76 r_work: 0.3293 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2205 Z= 0.158 Angle : 0.565 3.982 2997 Z= 0.326 Chirality : 0.051 0.132 354 Planarity : 0.003 0.031 366 Dihedral : 5.727 22.331 297 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.43 % Allowed : 18.80 % 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: -2.36 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 34 TYR 0.016 0.002 TYR A 114 PHE 0.012 0.002 PHE C 95 TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 2205) covalent geometry : angle 0.56517 / 0.33 ( 2997) hydrogen bonds : bond 0.02651 / 1.43 ( 35) hydrogen bonds : angle 5.80693 / 3.79 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.051 Fit side-chains REVERT: A 13 MET cc_start: 0.8133 (ttm) cc_final: 0.7706 (ttt) REVERT: A 104 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8089 (mtt90) REVERT: B 15 LYS cc_start: 0.8633 (mttt) cc_final: 0.8399 (mtpt) REVERT: B 104 ARG cc_start: 0.8791 (mtt180) cc_final: 0.8314 (mtt90) REVERT: C 61 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8336 (mtmm) REVERT: C 104 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8479 (mtt90) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.6174 time to fit residues: 32.5361 Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.119150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098514 restraints weight = 2313.493| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.77 r_work: 0.3288 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2205 Z= 0.167 Angle : 0.576 3.993 2997 Z= 0.332 Chirality : 0.051 0.133 354 Planarity : 0.003 0.032 366 Dihedral : 5.809 22.326 297 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.43 % Allowed : 19.23 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.016 0.002 TYR A 114 PHE 0.016 0.003 PHE B 33 TRP 0.002 0.001 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 2205) covalent geometry : angle 0.57611 / 0.33 ( 2997) hydrogen bonds : bond 0.02724 / 1.48 ( 35) hydrogen bonds : angle 5.84419 / 3.83 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.083 Fit side-chains REVERT: A 13 MET cc_start: 0.8136 (ttm) cc_final: 0.7714 (ttt) REVERT: A 104 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8100 (mtt90) REVERT: B 15 LYS cc_start: 0.8645 (mttt) cc_final: 0.8415 (mtpt) REVERT: B 104 ARG cc_start: 0.8792 (mtt180) cc_final: 0.8318 (mtt90) REVERT: C 61 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8373 (mtmm) REVERT: C 104 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8484 (mtt90) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.7847 time to fit residues: 41.3589 Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.117609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096641 restraints weight = 2343.420| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.79 r_work: 0.3252 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 2205 Z= 0.244 Angle : 0.643 4.016 2997 Z= 0.371 Chirality : 0.054 0.136 354 Planarity : 0.004 0.033 366 Dihedral : 6.135 21.991 297 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.43 % Allowed : 19.23 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 34 TYR 0.016 0.002 TYR B 114 PHE 0.015 0.003 PHE C 95 TRP 0.005 0.001 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.24 ( 2205) covalent geometry : angle 0.64289 / 0.37 ( 2997) hydrogen bonds : bond 0.03025 / 1.68 ( 35) hydrogen bonds : angle 6.08888 / 4.01 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.99 seconds wall clock time: 19 minutes 21.55 seconds (1161.55 seconds total)