Starting phenix.real_space_refine on Sat Apr 26 22:29:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j6j_0689/04_2025/6j6j_0689.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j6j_0689/04_2025/6j6j_0689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6j6j_0689/04_2025/6j6j_0689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j6j_0689/04_2025/6j6j_0689.map" model { file = "/net/cci-nas-00/data/ceres_data/6j6j_0689/04_2025/6j6j_0689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j6j_0689/04_2025/6j6j_0689.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 4 5.16 5 C 2264 2.51 5 N 628 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3624 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.74, per 1000 atoms: 0.76 Number of scatterers: 3624 At special positions: 0 Unit cell: (70.551, 60.021, 64.233, 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 4 16.00 O 728 8.00 N 628 7.00 C 2264 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: 0.88 Conformation dependent library (CDL) restraints added in 468.9 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.058A pdb=" N GLY A 41 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.058A pdb=" N GLY B 41 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.057A pdb=" N GLY C 41 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 21 removed outlier: 4.059A pdb=" N GLY D 41 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 492 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: 0.98 Time building geometry restraints manager: 1.03 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: 1159 1.34 - 1.46: 1020 1.46 - 1.57: 1517 1.57 - 1.69: 4 1.69 - 1.81: 4 Bond restraints: 3704 Sorted by residual: bond pdb=" C3 BTN C5100 " pdb=" O3 BTN C5100 " ideal model delta sigma weight residual 1.220 1.405 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C3 BTN D5100 " pdb=" O3 BTN D5100 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C3 BTN A5100 " pdb=" O3 BTN A5100 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C3 BTN B5100 " pdb=" O3 BTN B5100 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C2 BTN C5100 " pdb=" S1 BTN C5100 " ideal model delta sigma weight residual 1.824 1.663 0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 4656 1.68 - 3.37: 306 3.37 - 5.05: 71 5.05 - 6.73: 27 6.73 - 8.42: 8 Bond angle restraints: 5068 Sorted by residual: angle pdb=" C SER B 62 " pdb=" N ALA B 63 " pdb=" CA ALA B 63 " ideal model delta sigma weight residual 121.80 130.14 -8.34 2.44e+00 1.68e-01 1.17e+01 angle pdb=" C SER A 62 " pdb=" N ALA A 63 " pdb=" CA ALA A 63 " ideal model delta sigma weight residual 121.80 130.12 -8.32 2.44e+00 1.68e-01 1.16e+01 angle pdb=" C SER C 62 " pdb=" N ALA C 63 " pdb=" CA ALA C 63 " ideal model delta sigma weight residual 121.80 130.10 -8.30 2.44e+00 1.68e-01 1.16e+01 angle pdb=" C SER D 62 " pdb=" N ALA D 63 " pdb=" CA ALA D 63 " ideal model delta sigma weight residual 121.80 130.03 -8.23 2.44e+00 1.68e-01 1.14e+01 angle pdb=" C GLU A 51 " pdb=" N SER A 52 " pdb=" CA SER A 52 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 5063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 1724 13.87 - 27.74: 276 27.74 - 41.60: 52 41.60 - 55.47: 8 55.47 - 69.34: 4 Dihedral angle restraints: 2064 sinusoidal: 744 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA C 63 " pdb=" C ALA C 63 " pdb=" N PRO C 64 " pdb=" CA PRO C 64 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ALA D 63 " pdb=" C ALA D 63 " pdb=" N PRO D 64 " pdb=" CA PRO D 64 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ALA A 63 " pdb=" C ALA A 63 " pdb=" N PRO A 64 " pdb=" CA PRO A 64 " ideal model delta harmonic sigma weight residual 180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 2061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 421 0.057 - 0.114: 99 0.114 - 0.172: 40 0.172 - 0.229: 4 0.229 - 0.286: 4 Chirality restraints: 568 Sorted by residual: chirality pdb=" C2 BTN C5100 " pdb=" C4 BTN C5100 " pdb=" C7 BTN C5100 " pdb=" S1 BTN C5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2 BTN B5100 " pdb=" C4 BTN B5100 " pdb=" C7 BTN B5100 " pdb=" S1 BTN B5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2 BTN D5100 " pdb=" C4 BTN D5100 " pdb=" C7 BTN D5100 " pdb=" S1 BTN D5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 565 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTN B5100 " 0.002 2.00e-02 2.50e+03 3.58e-02 1.93e+01 pdb=" C4 BTN B5100 " -0.055 2.00e-02 2.50e+03 pdb=" C5 BTN B5100 " 0.046 2.00e-02 2.50e+03 pdb=" N1 BTN B5100 " -0.028 2.00e-02 2.50e+03 pdb=" N2 BTN B5100 " 0.041 2.00e-02 2.50e+03 pdb=" O3 BTN B5100 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN A5100 " 0.002 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" C4 BTN A5100 " -0.054 2.00e-02 2.50e+03 pdb=" C5 BTN A5100 " 0.046 2.00e-02 2.50e+03 pdb=" N1 BTN A5100 " -0.028 2.00e-02 2.50e+03 pdb=" N2 BTN A5100 " 0.041 2.00e-02 2.50e+03 pdb=" O3 BTN A5100 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN D5100 " -0.002 2.00e-02 2.50e+03 3.55e-02 1.90e+01 pdb=" C4 BTN D5100 " 0.054 2.00e-02 2.50e+03 pdb=" C5 BTN D5100 " -0.046 2.00e-02 2.50e+03 pdb=" N1 BTN D5100 " 0.029 2.00e-02 2.50e+03 pdb=" N2 BTN D5100 " -0.041 2.00e-02 2.50e+03 pdb=" O3 BTN D5100 " 0.006 2.00e-02 2.50e+03 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1171 2.81 - 3.33: 2720 3.33 - 3.86: 6145 3.86 - 4.38: 6884 4.38 - 4.90: 12906 Nonbonded interactions: 29826 Sorted by model distance: nonbonded pdb=" OH TYR C 43 " pdb=" O3 BTN C5100 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR D 43 " pdb=" O3 BTN D5100 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR B 43 " pdb=" O3 BTN B5100 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR A 43 " pdb=" O3 BTN A5100 " model vdw 2.292 3.040 nonbonded pdb=" ND2 ASN A 23 " pdb=" OG SER A 27 " model vdw 2.322 3.120 ... (remaining 29821 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.500 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 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 : 0.011 0.185 3704 Z= 0.524 Angle : 1.065 8.418 5068 Z= 0.564 Chirality : 0.061 0.286 568 Planarity : 0.005 0.036 632 Dihedral : 13.509 69.341 1240 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 19.77 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -1.47 (0.27), residues: 284 loop : -3.38 (0.35), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 75 HIS 0.002 0.001 HIS B 87 PHE 0.018 0.003 PHE A 29 TYR 0.016 0.002 TYR C 96 ARG 0.006 0.001 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.10890 ( 184) hydrogen bonds : angle 7.10031 ( 492) covalent geometry : bond 0.01066 ( 3704) covalent geometry : angle 1.06478 ( 5068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.353 Fit side-chains REVERT: A 105 ASN cc_start: 0.8185 (m110) cc_final: 0.7865 (m110) REVERT: B 105 ASN cc_start: 0.7803 (m110) cc_final: 0.7563 (m-40) REVERT: D 83 TYR cc_start: 0.7863 (m-10) cc_final: 0.7403 (m-10) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1953 time to fit residues: 15.8642 Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN B 81 ASN B 105 ASN B 107 GLN C 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.170051 restraints weight = 3813.844| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.77 r_work: 0.3871 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 0.027 3704 Z= 0.117 Angle : 0.602 6.936 5068 Z= 0.327 Chirality : 0.043 0.138 568 Planarity : 0.004 0.035 632 Dihedral : 6.131 26.862 592 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.23 % Allowed : 15.99 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.35), residues: 468 helix: None (None), residues: 0 sheet: -0.39 (0.31), residues: 228 loop : -2.96 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 92 HIS 0.001 0.000 HIS D 87 PHE 0.011 0.002 PHE C 29 TYR 0.010 0.002 TYR D 43 ARG 0.003 0.001 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 184) hydrogen bonds : angle 6.37309 ( 492) covalent geometry : bond 0.00259 ( 3704) covalent geometry : angle 0.60246 ( 5068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 115 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8962 (m) REVERT: C 118 ASN cc_start: 0.8456 (m-40) cc_final: 0.8242 (m110) outliers start: 18 outliers final: 7 residues processed: 67 average time/residue: 0.1630 time to fit residues: 13.4323 Evaluate side-chains 48 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146378 restraints weight = 3845.429| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.84 r_work: 0.3657 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 3704 Z= 0.249 Angle : 0.760 7.389 5068 Z= 0.408 Chirality : 0.047 0.161 568 Planarity : 0.007 0.069 632 Dihedral : 7.181 33.471 592 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.07 % Allowed : 18.31 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.21 (0.28), residues: 284 loop : -2.58 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 75 HIS 0.004 0.002 HIS A 127 PHE 0.017 0.004 PHE C 29 TYR 0.016 0.002 TYR C 43 ARG 0.007 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 184) hydrogen bonds : angle 6.82019 ( 492) covalent geometry : bond 0.00588 ( 3704) covalent geometry : angle 0.75968 ( 5068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.353 Fit side-chains REVERT: D 56 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7646 (pp) REVERT: D 107 GLN cc_start: 0.8485 (tt0) cc_final: 0.8190 (tt0) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.1610 time to fit residues: 12.2756 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.167272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151020 restraints weight = 3867.074| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.91 r_work: 0.3679 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3704 Z= 0.152 Angle : 0.632 7.422 5068 Z= 0.341 Chirality : 0.043 0.132 568 Planarity : 0.005 0.043 632 Dihedral : 6.313 29.340 592 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 5.52 % Allowed : 18.90 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -0.16 (0.32), residues: 220 loop : -2.76 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 75 HIS 0.003 0.002 HIS D 87 PHE 0.014 0.002 PHE B 29 TYR 0.009 0.002 TYR A 43 ARG 0.006 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 184) hydrogen bonds : angle 6.48993 ( 492) covalent geometry : bond 0.00354 ( 3704) covalent geometry : angle 0.63173 ( 5068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.483 Fit side-chains REVERT: A 131 THR cc_start: 0.8987 (m) cc_final: 0.8640 (p) outliers start: 19 outliers final: 16 residues processed: 62 average time/residue: 0.1490 time to fit residues: 11.5209 Evaluate side-chains 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.155569 restraints weight = 4122.025| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.95 r_work: 0.3694 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3704 Z= 0.243 Angle : 0.718 7.495 5068 Z= 0.382 Chirality : 0.046 0.157 568 Planarity : 0.006 0.047 632 Dihedral : 6.973 32.654 592 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 8.14 % Allowed : 17.73 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.92 (0.29), residues: 260 loop : -2.45 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 75 HIS 0.004 0.002 HIS D 87 PHE 0.016 0.003 PHE B 29 TYR 0.013 0.002 TYR A 43 ARG 0.004 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 184) hydrogen bonds : angle 6.79699 ( 492) covalent geometry : bond 0.00579 ( 3704) covalent geometry : angle 0.71782 ( 5068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.376 Fit side-chains outliers start: 28 outliers final: 26 residues processed: 71 average time/residue: 0.1457 time to fit residues: 12.9644 Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158863 restraints weight = 4104.822| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.01 r_work: 0.3709 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3704 Z= 0.167 Angle : 0.643 7.406 5068 Z= 0.344 Chirality : 0.044 0.134 568 Planarity : 0.005 0.044 632 Dihedral : 6.438 29.950 592 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 7.85 % Allowed : 18.02 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.19 (0.32), residues: 220 loop : -2.60 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 75 HIS 0.003 0.001 HIS A 87 PHE 0.014 0.002 PHE B 29 TYR 0.010 0.002 TYR A 43 ARG 0.003 0.001 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 184) hydrogen bonds : angle 6.63155 ( 492) covalent geometry : bond 0.00396 ( 3704) covalent geometry : angle 0.64334 ( 5068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.387 Fit side-chains outliers start: 27 outliers final: 25 residues processed: 66 average time/residue: 0.1521 time to fit residues: 12.5562 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.158394 restraints weight = 4081.626| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.07 r_work: 0.3706 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3704 Z= 0.165 Angle : 0.625 7.196 5068 Z= 0.335 Chirality : 0.043 0.136 568 Planarity : 0.005 0.040 632 Dihedral : 6.375 29.704 592 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 8.43 % Allowed : 17.44 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.14 (0.32), residues: 220 loop : -2.52 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 75 HIS 0.003 0.002 HIS D 87 PHE 0.014 0.002 PHE B 29 TYR 0.010 0.002 TYR A 43 ARG 0.003 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 184) hydrogen bonds : angle 6.60713 ( 492) covalent geometry : bond 0.00389 ( 3704) covalent geometry : angle 0.62532 ( 5068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.400 Fit side-chains REVERT: D 56 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7909 (pp) REVERT: D 62 SER cc_start: 0.7928 (m) cc_final: 0.7449 (p) outliers start: 29 outliers final: 26 residues processed: 69 average time/residue: 0.1407 time to fit residues: 12.4060 Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160201 restraints weight = 4005.817| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.93 r_work: 0.3738 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3704 Z= 0.118 Angle : 0.562 5.879 5068 Z= 0.305 Chirality : 0.041 0.130 568 Planarity : 0.004 0.040 632 Dihedral : 5.919 28.710 592 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 8.14 % Allowed : 18.60 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.39), residues: 468 helix: None (None), residues: 0 sheet: -0.19 (0.32), residues: 224 loop : -2.33 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 108 HIS 0.002 0.001 HIS D 87 PHE 0.014 0.002 PHE A 29 TYR 0.010 0.001 TYR C 96 ARG 0.003 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 184) hydrogen bonds : angle 6.44814 ( 492) covalent geometry : bond 0.00274 ( 3704) covalent geometry : angle 0.56167 ( 5068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 49 time to evaluate : 0.359 Fit side-chains REVERT: A 62 SER cc_start: 0.8000 (m) cc_final: 0.7314 (p) REVERT: A 131 THR cc_start: 0.9097 (m) cc_final: 0.8796 (p) REVERT: B 62 SER cc_start: 0.7616 (m) cc_final: 0.7171 (p) REVERT: C 62 SER cc_start: 0.7988 (m) cc_final: 0.7554 (p) REVERT: D 53 ARG cc_start: 0.8639 (ttm170) cc_final: 0.8372 (ttp-170) outliers start: 28 outliers final: 24 residues processed: 68 average time/residue: 0.1481 time to fit residues: 12.6636 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.172228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157238 restraints weight = 3995.972| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.88 r_work: 0.3720 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3704 Z= 0.203 Angle : 0.633 6.200 5068 Z= 0.339 Chirality : 0.044 0.135 568 Planarity : 0.005 0.038 632 Dihedral : 6.346 30.275 592 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 8.43 % Allowed : 17.73 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.39), residues: 468 helix: None (None), residues: 0 sheet: -0.83 (0.29), residues: 260 loop : -2.16 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 108 HIS 0.004 0.002 HIS A 87 PHE 0.015 0.003 PHE C 29 TYR 0.012 0.002 TYR A 43 ARG 0.003 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 184) hydrogen bonds : angle 6.67344 ( 492) covalent geometry : bond 0.00485 ( 3704) covalent geometry : angle 0.63329 ( 5068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.355 Fit side-chains REVERT: C 62 SER cc_start: 0.8065 (m) cc_final: 0.7757 (p) REVERT: D 53 ARG cc_start: 0.8669 (ttm170) cc_final: 0.8407 (ttp-170) outliers start: 29 outliers final: 28 residues processed: 69 average time/residue: 0.1334 time to fit residues: 11.7627 Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 0.0970 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.170469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154871 restraints weight = 4132.894| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.94 r_work: 0.3679 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3704 Z= 0.266 Angle : 0.696 6.841 5068 Z= 0.370 Chirality : 0.047 0.147 568 Planarity : 0.006 0.042 632 Dihedral : 6.748 31.856 592 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 8.14 % Allowed : 18.60 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.20 (0.27), residues: 284 loop : -2.43 (0.51), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 108 HIS 0.005 0.002 HIS A 87 PHE 0.017 0.003 PHE C 29 TYR 0.014 0.002 TYR B 43 ARG 0.004 0.001 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 184) hydrogen bonds : angle 6.88442 ( 492) covalent geometry : bond 0.00636 ( 3704) covalent geometry : angle 0.69581 ( 5068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.388 Fit side-chains REVERT: D 53 ARG cc_start: 0.8640 (ttm170) cc_final: 0.8373 (ttp-170) outliers start: 28 outliers final: 26 residues processed: 69 average time/residue: 0.1376 time to fit residues: 12.1830 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160899 restraints weight = 4043.308| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.94 r_work: 0.3735 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3704 Z= 0.128 Angle : 0.558 5.475 5068 Z= 0.303 Chirality : 0.041 0.127 568 Planarity : 0.004 0.042 632 Dihedral : 5.871 28.510 592 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 7.27 % Allowed : 19.77 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -0.90 (0.28), residues: 268 loop : -2.70 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.001 HIS D 87 PHE 0.014 0.002 PHE A 29 TYR 0.010 0.001 TYR C 96 ARG 0.003 0.000 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 184) hydrogen bonds : angle 6.55373 ( 492) covalent geometry : bond 0.00305 ( 3704) covalent geometry : angle 0.55762 ( 5068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.41 seconds wall clock time: 33 minutes 31.76 seconds (2011.76 seconds total)