Starting phenix.real_space_refine on Tue Aug 4 12:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9j_65779/08_2026/9w9j_65779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9j_65779/08_2026/9w9j_65779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9j_65779/08_2026/9w9j_65779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9j_65779/08_2026/9w9j_65779.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9j_65779/08_2026/9w9j_65779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9j_65779/08_2026/9w9j_65779.cif" } resolution = 2.49 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= 0.002 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 6 5.16 5 C 1413 2.51 5 N 363 2.21 5 O 405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 2187 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Restraints were copied for chains: A, C Time building chain proxies: 0.68, per 1000 atoms: 0.31 Number of scatterers: 2187 At special positions: 0 Unit cell: (81.84, 70.68, 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 6 16.00 O 405 8.00 N 363 7.00 C 1413 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: 0.18 Conformation dependent library (CDL) restraints added in 87.1 milliseconds 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 40.9% 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 'A' and resid 14 through 16 removed outlier: 6.245A pdb=" N LYS B 15 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.260A pdb=" N VAL B 20 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 30 removed outlier: 6.348A pdb=" N ALA B 25 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL A 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASN B 27 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET A 30 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 29 " --> pdb=" O MET A 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.662A pdb=" N PHE B 33 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 57 through 62 removed outlier: 6.108A pdb=" N LEU B 58 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLU A 61 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR B 60 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 58 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.273A pdb=" N VAL B 65 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.321A pdb=" N VAL B 71 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 76 through 80 removed outlier: 6.815A pdb=" N SER B 77 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR A 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N LYS B 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N TRP C 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N TYR B 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 92 through 97 removed outlier: 6.254A pdb=" N GLU B 92 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE C 95 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 94 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA C 97 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 96 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 110 removed outlier: 6.214A pdb=" N TYR B 105 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA A 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ILE B 107 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N ALA B 109 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA C 109 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 110 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.863A pdb=" N TYR B 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.731A pdb=" N THR B 118 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL A 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 120 " --> pdb=" O VAL A 121 " (cutoff:3.500A) 33 hydrogen bonds defined for protein. 99 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: 0.25 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: 684 1.34 - 1.45: 347 1.45 - 1.57: 1198 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 2241 Sorted by residual: bond pdb=" CA PHE B 33 " pdb=" CB PHE B 33 " ideal model delta sigma weight residual 1.532 1.557 -0.025 1.68e-02 3.54e+03 2.16e+00 bond pdb=" CA PHE C 33 " pdb=" CB PHE C 33 " ideal model delta sigma weight residual 1.532 1.557 -0.025 1.68e-02 3.54e+03 2.15e+00 bond pdb=" CA PHE A 33 " pdb=" CB PHE A 33 " ideal model delta sigma weight residual 1.532 1.556 -0.024 1.68e-02 3.54e+03 2.06e+00 bond pdb=" CB PHE B 33 " pdb=" CG PHE B 33 " ideal model delta sigma weight residual 1.502 1.532 -0.030 2.30e-02 1.89e+03 1.70e+00 bond pdb=" CB PHE C 33 " pdb=" CG PHE C 33 " ideal model delta sigma weight residual 1.502 1.532 -0.030 2.30e-02 1.89e+03 1.68e+00 ... (remaining 2236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 2856 1.57 - 3.13: 157 3.13 - 4.70: 26 4.70 - 6.27: 3 6.27 - 7.84: 3 Bond angle restraints: 3045 Sorted by residual: angle pdb=" CA PHE A 33 " pdb=" CB PHE A 33 " pdb=" CG PHE A 33 " ideal model delta sigma weight residual 113.80 117.02 -3.22 1.00e+00 1.00e+00 1.04e+01 angle pdb=" CA PHE C 33 " pdb=" CB PHE C 33 " pdb=" CG PHE C 33 " ideal model delta sigma weight residual 113.80 116.97 -3.17 1.00e+00 1.00e+00 1.00e+01 angle pdb=" CA PHE B 33 " pdb=" CB PHE B 33 " pdb=" CG PHE B 33 " ideal model delta sigma weight residual 113.80 116.96 -3.16 1.00e+00 1.00e+00 9.99e+00 angle pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 113.90 118.82 -4.92 1.80e+00 3.09e-01 7.47e+00 angle pdb=" CA TYR A 114 " pdb=" CB TYR A 114 " pdb=" CG TYR A 114 " ideal model delta sigma weight residual 113.90 118.78 -4.88 1.80e+00 3.09e-01 7.36e+00 ... (remaining 3040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.89: 1053 11.89 - 23.78: 153 23.78 - 35.67: 72 35.67 - 47.56: 24 47.56 - 59.45: 18 Dihedral angle restraints: 1320 sinusoidal: 504 harmonic: 816 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 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+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 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+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 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 1317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 161 0.032 - 0.065: 103 0.065 - 0.097: 67 0.097 - 0.129: 20 0.129 - 0.161: 3 Chirality restraints: 354 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CB ILE A 26 " pdb=" CA ILE A 26 " pdb=" CG1 ILE A 26 " pdb=" CG2 ILE A 26 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB ILE C 26 " pdb=" CA ILE C 26 " pdb=" CG1 ILE C 26 " pdb=" CG2 ILE C 26 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 351 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " -0.012 2.00e-02 2.50e+03 9.74e-03 1.90e+00 pdb=" CG TYR C 114 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR C 114 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 114 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " -0.012 2.00e-02 2.50e+03 9.65e-03 1.86e+00 pdb=" CG TYR B 114 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.000 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 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " -0.012 2.00e-02 2.50e+03 9.55e-03 1.82e+00 pdb=" CG TYR A 114 " 0.023 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 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " -0.001 2.00e-02 2.50e+03 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 252 2.75 - 3.29: 1916 3.29 - 3.83: 3837 3.83 - 4.36: 4278 4.36 - 4.90: 8236 Nonbonded interactions: 18519 Sorted by model distance: nonbonded pdb=" OH TYR B 105 " pdb=" OD2 ASP C 74 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP B 74 " pdb=" OH TYR A 105 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR B 114 " pdb=" OG1 THR C 119 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR B 119 " pdb=" OH TYR A 114 " model vdw 2.289 3.040 nonbonded pdb=" O THR B 59 " pdb=" OG1 THR B 59 " model vdw 2.459 3.040 ... (remaining 18514 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 'B' selection = chain 'A' 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: 3.800 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: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.080 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:5.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 2241 Z= 0.260 Angle : 0.805 7.836 3045 Z= 0.453 Chirality : 0.055 0.161 354 Planarity : 0.006 0.046 375 Dihedral : 16.038 59.450 792 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 29.11 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.42), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.32), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG B 104 TYR 0.024 0.002 TYR C 114 PHE 0.008 0.003 PHE C 87 TRP 0.004 0.001 TRP B 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 ( 2241) covalent geometry : angle 0.80509 / 0.45 ( 3045) hydrogen bonds : bond 0.14966 / 9.70 ( 33) hydrogen bonds : angle 9.56024 / 6.54 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.049 Fit side-chains REVERT: B 21 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7463 (ttm-80) REVERT: B 92 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8076 (mt-10) REVERT: B 104 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8273 (mtt-85) REVERT: C 21 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7142 (ttp-110) REVERT: C 74 ASP cc_start: 0.9056 (t0) cc_final: 0.8773 (t0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.4541 time to fit residues: 23.0852 Evaluate side-chains 49 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.049 ------------------------------------------------------------------------------- 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: 0.0020 chunk 24 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN A 98 ASN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.135049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107939 restraints weight = 2400.422| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.07 r_work: 0.3492 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2241 Z= 0.107 Angle : 0.485 3.070 3045 Z= 0.272 Chirality : 0.048 0.122 354 Planarity : 0.004 0.028 375 Dihedral : 5.283 16.316 300 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.11 % Allowed : 20.68 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.44), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 104 TYR 0.014 0.001 TYR A 114 PHE 0.027 0.002 PHE B 33 TRP 0.001 0.001 TRP B 79 HIS 0.002 0.000 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 2241) covalent geometry : angle 0.48489 / 0.27 ( 3045) hydrogen bonds : bond 0.02457 / 1.61 ( 33) hydrogen bonds : angle 6.52815 / 4.53 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.082 Fit side-chains REVERT: B 21 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7326 (ttp-110) REVERT: B 104 ARG cc_start: 0.8503 (mtt90) cc_final: 0.8264 (mtt-85) REVERT: C 21 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7356 (ttp-110) outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 0.5283 time to fit residues: 25.8147 Evaluate side-chains 47 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099208 restraints weight = 2392.548| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.02 r_work: 0.3358 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2241 Z= 0.196 Angle : 0.553 3.390 3045 Z= 0.309 Chirality : 0.048 0.125 354 Planarity : 0.003 0.023 375 Dihedral : 5.672 20.059 300 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.80 % Allowed : 18.99 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.43), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 104 TYR 0.017 0.002 TYR B 114 PHE 0.027 0.003 PHE B 33 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 2241) covalent geometry : angle 0.55314 / 0.31 ( 3045) hydrogen bonds : bond 0.02789 / 1.84 ( 33) hydrogen bonds : angle 6.05220 / 4.25 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.084 Fit side-chains REVERT: B 21 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7485 (ttp-110) REVERT: B 104 ARG cc_start: 0.8439 (mtt90) cc_final: 0.8151 (mtt-85) REVERT: C 21 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7450 (ttp-110) outliers start: 9 outliers final: 1 residues processed: 47 average time/residue: 0.5756 time to fit residues: 27.5238 Evaluate side-chains 43 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.127984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.100829 restraints weight = 2344.616| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.01 r_work: 0.3398 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2241 Z= 0.155 Angle : 0.511 3.348 3045 Z= 0.289 Chirality : 0.047 0.123 354 Planarity : 0.003 0.025 375 Dihedral : 5.485 18.235 300 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.53 % Allowed : 18.99 % Favored : 78.48 % 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: -2.74 (0.43), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 104 TYR 0.015 0.002 TYR B 114 PHE 0.028 0.002 PHE B 33 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 2241) covalent geometry : angle 0.51101 / 0.29 ( 3045) hydrogen bonds : bond 0.02324 / 1.61 ( 33) hydrogen bonds : angle 5.71238 / 3.99 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.083 Fit side-chains REVERT: B 21 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7529 (ttp-110) REVERT: B 104 ARG cc_start: 0.8441 (mtt90) cc_final: 0.8171 (mtt-85) REVERT: C 21 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7450 (ttp-110) outliers start: 6 outliers final: 0 residues processed: 43 average time/residue: 0.6172 time to fit residues: 27.0041 Evaluate side-chains 42 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.131634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106597 restraints weight = 2413.709| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.94 r_work: 0.3506 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2241 Z= 0.100 Angle : 0.460 3.199 3045 Z= 0.261 Chirality : 0.046 0.121 354 Planarity : 0.003 0.024 375 Dihedral : 5.094 17.121 300 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.11 % Allowed : 20.25 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.43), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 104 TYR 0.012 0.001 TYR B 114 PHE 0.027 0.002 PHE B 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 0.00234 / 0.10 ( 2241) covalent geometry : angle 0.46012 / 0.26 ( 3045) hydrogen bonds : bond 0.02015 / 1.40 ( 33) hydrogen bonds : angle 5.49992 / 3.78 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.061 Fit side-chains REVERT: B 21 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7473 (ttp-110) REVERT: B 104 ARG cc_start: 0.8430 (mtt90) cc_final: 0.8151 (mtt-85) REVERT: C 21 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7455 (ttp-110) REVERT: C 74 ASP cc_start: 0.8955 (t0) cc_final: 0.8699 (t0) outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 0.6248 time to fit residues: 29.2568 Evaluate side-chains 45 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain A residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.134555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108615 restraints weight = 2338.364| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.00 r_work: 0.3530 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2241 Z= 0.091 Angle : 0.448 3.165 3045 Z= 0.253 Chirality : 0.046 0.119 354 Planarity : 0.002 0.016 375 Dihedral : 4.878 16.725 300 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.11 % Allowed : 20.68 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.44), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.012 0.001 TYR B 114 PHE 0.029 0.002 PHE B 33 TRP 0.001 0.000 TRP A 79 HIS 0.001 0.000 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 2241) covalent geometry : angle 0.44794 / 0.25 ( 3045) hydrogen bonds : bond 0.01880 / 1.30 ( 33) hydrogen bonds : angle 5.30055 / 3.62 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.082 Fit side-chains REVERT: B 21 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7467 (ttp-110) REVERT: C 21 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7428 (ttp-110) REVERT: C 74 ASP cc_start: 0.8875 (t0) cc_final: 0.8666 (t0) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.5812 time to fit residues: 26.6892 Evaluate side-chains 43 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.126518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099663 restraints weight = 2361.216| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.02 r_work: 0.3375 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2241 Z= 0.180 Angle : 0.520 3.440 3045 Z= 0.293 Chirality : 0.047 0.124 354 Planarity : 0.003 0.018 375 Dihedral : 5.372 19.295 300 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.11 % Allowed : 20.68 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.45), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.017 0.002 TYR B 114 PHE 0.030 0.003 PHE B 33 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 2241) covalent geometry : angle 0.52020 / 0.29 ( 3045) hydrogen bonds : bond 0.02211 / 1.54 ( 33) hydrogen bonds : angle 5.48456 / 3.77 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.066 Fit side-chains REVERT: B 21 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7760 (ttm-80) REVERT: C 21 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7340 (ttp-110) outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 0.6367 time to fit residues: 26.5740 Evaluate side-chains 43 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain C residue 30 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.131911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.105717 restraints weight = 2338.754| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.00 r_work: 0.3478 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2241 Z= 0.102 Angle : 0.462 3.237 3045 Z= 0.262 Chirality : 0.047 0.120 354 Planarity : 0.002 0.017 375 Dihedral : 5.041 17.549 300 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.27 % Allowed : 21.52 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.45), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.013 0.001 TYR B 114 PHE 0.032 0.002 PHE B 33 TRP 0.001 0.000 TRP A 79 HIS 0.001 0.000 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 2241) covalent geometry : angle 0.46177 / 0.26 ( 3045) hydrogen bonds : bond 0.01953 / 1.37 ( 33) hydrogen bonds : angle 5.32854 / 3.65 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.053 Fit side-chains REVERT: B 21 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7491 (ttp-110) REVERT: C 21 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7449 (ttp-110) REVERT: C 74 ASP cc_start: 0.8955 (t0) cc_final: 0.8705 (t0) outliers start: 3 outliers final: 0 residues processed: 44 average time/residue: 0.5024 time to fit residues: 22.4786 Evaluate side-chains 43 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.125059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097980 restraints weight = 2408.643| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.04 r_work: 0.3360 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2241 Z= 0.205 Angle : 0.542 3.484 3045 Z= 0.305 Chirality : 0.048 0.126 354 Planarity : 0.003 0.018 375 Dihedral : 5.570 19.797 300 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.27 % Allowed : 21.94 % Favored : 76.79 % 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: -2.43 (0.45), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 104 TYR 0.018 0.002 TYR B 114 PHE 0.035 0.003 PHE B 33 TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 ( 2241) covalent geometry : angle 0.54198 / 0.30 ( 3045) hydrogen bonds : bond 0.02351 / 1.64 ( 33) hydrogen bonds : angle 5.51687 / 3.79 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.050 Fit side-chains REVERT: B 21 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7748 (ttm-80) REVERT: A 21 ARG cc_start: 0.8787 (mtp85) cc_final: 0.8407 (ttm-80) REVERT: C 21 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7361 (ttp-110) REVERT: C 74 ASP cc_start: 0.9109 (t0) cc_final: 0.8844 (t0) REVERT: C 92 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8430 (mt-10) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.4810 time to fit residues: 22.9481 Evaluate side-chains 49 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain C residue 30 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.130416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.104102 restraints weight = 2375.955| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.01 r_work: 0.3448 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2241 Z= 0.112 Angle : 0.477 3.308 3045 Z= 0.270 Chirality : 0.047 0.121 354 Planarity : 0.003 0.020 375 Dihedral : 5.197 17.930 300 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.42 % Allowed : 23.63 % Favored : 75.95 % 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: -2.40 (0.45), residues: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 104 TYR 0.013 0.001 TYR B 114 PHE 0.030 0.002 PHE B 33 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.000 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 2241) covalent geometry : angle 0.47750 / 0.27 ( 3045) hydrogen bonds : bond 0.02024 / 1.43 ( 33) hydrogen bonds : angle 5.33726 / 3.65 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.052 Fit side-chains REVERT: C 21 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7490 (ttp-110) REVERT: C 74 ASP cc_start: 0.8998 (t0) cc_final: 0.8732 (t0) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.4593 time to fit residues: 19.6161 Evaluate side-chains 42 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.0070 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.0604 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.128779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102154 restraints weight = 2420.116| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.04 r_work: 0.3427 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2241 Z= 0.132 Angle : 0.503 4.384 3045 Z= 0.282 Chirality : 0.047 0.122 354 Planarity : 0.004 0.048 375 Dihedral : 5.272 18.458 300 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.84 % Allowed : 23.21 % Favored : 75.95 % 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: 267 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 21 TYR 0.015 0.001 TYR B 114 PHE 0.034 0.003 PHE B 33 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 2241) covalent geometry : angle 0.50299 / 0.28 ( 3045) hydrogen bonds : bond 0.02084 / 1.47 ( 33) hydrogen bonds : angle 5.32887 / 3.64 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1053.43 seconds wall clock time: 18 minutes 36.26 seconds (1116.26 seconds total)