Starting phenix.real_space_refine on Tue Feb 11 01:59:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j6j_0689/02_2025/6j6j_0689.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j6j_0689/02_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_0689/02_2025/6j6j_0689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j6j_0689/02_2025/6j6j_0689.map" model { file = "/net/cci-nas-00/data/ceres_data/6j6j_0689/02_2025/6j6j_0689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j6j_0689/02_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-5592/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: 2.63, per 1000 atoms: 0.73 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: 0.93 Conformation dependent library (CDL) restraints added in 468.8 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: 0.38 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: 1.01 Time building geometry restraints manager: 0.98 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- 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= 0.686 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 *********************** 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 : 0.486 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: 0.2057 time to fit residues: 16.6738 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 : 0.377 ------------------------------------------------------------------------------- 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 = 0.170048 restraints weight = 3813.844| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.77 r_work: 0.3879 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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= 0.172 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 *********************** 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: 0.9137 (OUTLIER) cc_final: 0.8916 (m) outliers start: 18 outliers final: 7 residues processed: 67 average time/residue: 0.1730 time to fit residues: 14.3135 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 : 0.381 ------------------------------------------------------------------------------- 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: 0.3980 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 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: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.160857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145312 restraints weight = 3856.581| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.84 r_work: 0.3662 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3704 Z= 0.376 Angle : 0.750 7.569 5068 Z= 0.404 Chirality : 0.047 0.161 568 Planarity : 0.006 0.070 632 Dihedral : 7.130 33.546 592 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.07 % Allowed : 18.60 % Favored : 77.33 % 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: -2.67 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.20 (0.28), residues: 284 loop : -2.57 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 75 HIS 0.004 0.002 HIS D 87 PHE 0.017 0.004 PHE C 29 TYR 0.015 0.002 TYR C 43 ARG 0.009 0.001 ARG A 84 *********************** 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 : 0.359 Fit side-chains REVERT: D 56 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7659 (pp) REVERT: D 107 GLN cc_start: 0.8485 (tt0) cc_final: 0.8188 (tt0) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.1526 time to fit residues: 11.6276 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 : 0.369 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.168498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152350 restraints weight = 3922.310| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.93 r_work: 0.3646 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3704 Z= 0.252 Angle : 0.640 7.569 5068 Z= 0.346 Chirality : 0.044 0.133 568 Planarity : 0.005 0.043 632 Dihedral : 6.420 30.068 592 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 5.52 % Allowed : 19.19 % Favored : 75.29 % 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: -2.17 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -0.18 (0.32), residues: 220 loop : -2.77 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 75 HIS 0.004 0.002 HIS D 87 PHE 0.014 0.003 PHE B 29 TYR 0.010 0.002 TYR A 43 ARG 0.002 0.000 ARG B 84 *********************** 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 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.354 Fit side-chains REVERT: D 56 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7768 (pp) outliers start: 19 outliers final: 16 residues processed: 62 average time/residue: 0.1507 time to fit residues: 11.7242 Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 56 LEU 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: 2.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 0.0370 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.166055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152753 restraints weight = 3917.058| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.55 r_work: 0.3671 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3704 Z= 0.322 Angle : 0.671 7.586 5068 Z= 0.359 Chirality : 0.045 0.148 568 Planarity : 0.005 0.043 632 Dihedral : 6.691 31.584 592 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 7.85 % Allowed : 18.31 % 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: -2.50 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.88 (0.29), residues: 264 loop : -2.71 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 75 HIS 0.004 0.002 HIS D 87 PHE 0.016 0.003 PHE B 29 TYR 0.011 0.002 TYR B 43 ARG 0.005 0.001 ARG A 84 *********************** 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 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.579 Fit side-chains REVERT: C 61 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8186 (p0) outliers start: 27 outliers final: 22 residues processed: 67 average time/residue: 0.1427 time to fit residues: 12.2879 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.165134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151951 restraints weight = 3936.879| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.54 r_work: 0.3647 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 3704 Z= 0.397 Angle : 0.719 7.479 5068 Z= 0.381 Chirality : 0.047 0.149 568 Planarity : 0.006 0.046 632 Dihedral : 6.904 32.007 592 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % 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: -2.64 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.25 (0.27), residues: 284 loop : -2.40 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 108 HIS 0.005 0.002 HIS D 87 PHE 0.016 0.003 PHE B 29 TYR 0.014 0.002 TYR B 43 ARG 0.003 0.001 ARG A 84 *********************** 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 80 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 0.398 Fit side-chains outliers start: 29 outliers final: 29 residues processed: 72 average time/residue: 0.1348 time to fit residues: 12.4198 Evaluate side-chains 79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 61 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.175652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159186 restraints weight = 4051.355| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.03 r_work: 0.3717 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3704 Z= 0.203 Angle : 0.607 7.240 5068 Z= 0.325 Chirality : 0.042 0.130 568 Planarity : 0.004 0.041 632 Dihedral : 6.196 28.524 592 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 7.85 % Allowed : 18.90 % 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: -2.39 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.79 (0.28), residues: 264 loop : -2.68 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 108 HIS 0.003 0.001 HIS D 87 PHE 0.015 0.002 PHE A 29 TYR 0.011 0.002 TYR C 60 ARG 0.003 0.000 ARG A 84 *********************** 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 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.377 Fit side-chains REVERT: D 62 SER cc_start: 0.7897 (m) cc_final: 0.7502 (p) outliers start: 27 outliers final: 24 residues processed: 64 average time/residue: 0.1433 time to fit residues: 11.7236 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.180288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.163846 restraints weight = 4017.442| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.00 r_work: 0.3759 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3704 Z= 0.156 Angle : 0.551 6.737 5068 Z= 0.299 Chirality : 0.041 0.130 568 Planarity : 0.004 0.038 632 Dihedral : 5.693 27.887 592 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 6.98 % Allowed : 20.35 % Favored : 72.67 % 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: -1.90 (0.39), residues: 468 helix: None (None), residues: 0 sheet: -0.39 (0.31), residues: 232 loop : -2.21 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 75 HIS 0.002 0.001 HIS D 87 PHE 0.014 0.002 PHE A 29 TYR 0.010 0.001 TYR B 96 ARG 0.003 0.000 ARG D 84 *********************** 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 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.7751 (m) cc_final: 0.7133 (p) REVERT: B 62 SER cc_start: 0.7629 (m) cc_final: 0.7086 (p) REVERT: C 53 ARG cc_start: 0.8635 (mtt90) cc_final: 0.8424 (ttm170) REVERT: C 107 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: D 53 ARG cc_start: 0.8639 (ttm170) cc_final: 0.8378 (ttp-170) outliers start: 24 outliers final: 20 residues processed: 63 average time/residue: 0.1659 time to fit residues: 12.8926 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 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 118 ASN 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 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: 8.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.173474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158097 restraints weight = 4022.204| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.92 r_work: 0.3717 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3704 Z= 0.289 Angle : 0.637 5.915 5068 Z= 0.343 Chirality : 0.044 0.134 568 Planarity : 0.005 0.039 632 Dihedral : 6.271 30.920 592 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 8.72 % Allowed : 18.60 % Favored : 72.67 % 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: -2.22 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.67 (0.28), residues: 264 loop : -2.57 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 75 HIS 0.004 0.002 HIS A 87 PHE 0.014 0.003 PHE B 29 TYR 0.011 0.002 TYR D 60 ARG 0.006 0.001 ARG C 84 *********************** 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 79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 0.363 Fit side-chains REVERT: A 53 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8158 (ttp-170) REVERT: B 62 SER cc_start: 0.7641 (m) cc_final: 0.7126 (p) REVERT: C 56 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7806 (pp) REVERT: D 53 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8434 (ttp-170) outliers start: 30 outliers final: 25 residues processed: 71 average time/residue: 0.1422 time to fit residues: 12.6467 Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 56 LEU 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 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: 0.9990 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.171863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156742 restraints weight = 4096.842| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.91 r_work: 0.3709 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3704 Z= 0.333 Angle : 0.663 6.206 5068 Z= 0.358 Chirality : 0.045 0.137 568 Planarity : 0.005 0.069 632 Dihedral : 6.432 30.957 592 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 7.56 % Allowed : 20.93 % Favored : 71.51 % 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 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.06 (0.27), residues: 284 loop : -2.36 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 75 HIS 0.004 0.002 HIS A 87 PHE 0.015 0.003 PHE C 29 TYR 0.017 0.002 TYR D 60 ARG 0.006 0.001 ARG C 84 ********************** 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 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.366 Fit side-chains REVERT: B 62 SER cc_start: 0.7685 (m) cc_final: 0.7309 (t) REVERT: C 56 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7808 (pp) REVERT: C 62 SER cc_start: 0.8015 (m) cc_final: 0.7636 (p) REVERT: C 84 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7906 (ttm-80) REVERT: D 53 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8414 (ttp-170) outliers start: 26 outliers final: 25 residues processed: 69 average time/residue: 0.1476 time to fit residues: 12.7911 Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 56 LEU 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 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: 7.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.173015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158128 restraints weight = 4044.270| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.89 r_work: 0.3726 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3704 Z= 0.260 Angle : 0.614 5.782 5068 Z= 0.335 Chirality : 0.043 0.132 568 Planarity : 0.005 0.058 632 Dihedral : 6.033 29.230 592 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 7.85 % Allowed : 21.22 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.39 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -0.76 (0.28), residues: 264 loop : -2.72 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 75 HIS 0.004 0.002 HIS A 87 PHE 0.014 0.002 PHE B 29 TYR 0.015 0.002 TYR D 60 ARG 0.006 0.001 ARG C 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.33 seconds wall clock time: 34 minutes 9.78 seconds (2049.78 seconds total)