Starting phenix.real_space_refine on Fri May 9 14:55:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k24_61989/05_2025/9k24_61989.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k24_61989/05_2025/9k24_61989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k24_61989/05_2025/9k24_61989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k24_61989/05_2025/9k24_61989.map" model { file = "/net/cci-nas-00/data/ceres_data/9k24_61989/05_2025/9k24_61989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k24_61989/05_2025/9k24_61989.cif" } resolution = 3.6 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1680 2.51 5 N 468 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2682 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 447 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.06, per 1000 atoms: 0.77 Number of scatterers: 2682 At special positions: 0 Unit cell: (133.63, 82.17, 31.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 534 8.00 N 468 7.00 C 1680 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: 0.63 Conformation dependent library (CDL) restraints added in 410.3 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 44 removed outlier: 6.721A pdb=" N GLU B 35 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU A 38 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 37 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N VAL A 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR B 39 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N SER A 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY B 41 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR A 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS B 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY B 36 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR C 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLY C 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.426A pdb=" N VAL B 48 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.470A pdb=" N GLU B 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 72 removed outlier: 6.336A pdb=" N VAL B 71 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.462A pdb=" N THR B 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 35 through 44 removed outlier: 6.726A pdb=" N GLU E 35 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU D 38 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL E 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL D 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR E 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER D 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY E 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR D 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS E 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLY E 36 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TYR F 39 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLY F 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 49 removed outlier: 6.445A pdb=" N VAL E 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 63 removed outlier: 6.489A pdb=" N GLU E 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN E 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 70 through 72 removed outlier: 6.322A pdb=" N VAL E 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 81 through 82 removed outlier: 6.473A pdb=" N THR E 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) 16 hydrogen bonds defined for protein. 48 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: 0.57 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 468 1.29 - 1.35: 420 1.35 - 1.42: 96 1.42 - 1.48: 438 1.48 - 1.54: 1272 Bond restraints: 2694 Sorted by residual: bond pdb=" N GLY E 51 " pdb=" CA GLY E 51 " ideal model delta sigma weight residual 1.445 1.450 -0.006 8.30e-03 1.45e+04 5.03e-01 bond pdb=" N GLY B 51 " pdb=" CA GLY B 51 " ideal model delta sigma weight residual 1.445 1.450 -0.006 8.30e-03 1.45e+04 4.42e-01 bond pdb=" N GLY A 51 " pdb=" CA GLY A 51 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.78e-01 bond pdb=" N GLY C 51 " pdb=" CA GLY C 51 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.71e-01 bond pdb=" CA VAL C 95 " pdb=" CB VAL C 95 " ideal model delta sigma weight residual 1.535 1.542 -0.007 1.24e-02 6.50e+03 3.59e-01 ... (remaining 2689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 3362 0.96 - 1.92: 214 1.92 - 2.88: 24 2.88 - 3.84: 30 3.84 - 4.80: 6 Bond angle restraints: 3636 Sorted by residual: angle pdb=" N GLY F 51 " pdb=" CA GLY F 51 " pdb=" C GLY F 51 " ideal model delta sigma weight residual 111.20 114.28 -3.08 1.39e+00 5.18e-01 4.92e+00 angle pdb=" N GLY E 51 " pdb=" CA GLY E 51 " pdb=" C GLY E 51 " ideal model delta sigma weight residual 111.20 114.28 -3.08 1.39e+00 5.18e-01 4.91e+00 angle pdb=" N GLY D 51 " pdb=" CA GLY D 51 " pdb=" C GLY D 51 " ideal model delta sigma weight residual 111.20 114.26 -3.06 1.39e+00 5.18e-01 4.85e+00 angle pdb=" N GLY C 51 " pdb=" CA GLY C 51 " pdb=" C GLY C 51 " ideal model delta sigma weight residual 111.20 114.26 -3.06 1.39e+00 5.18e-01 4.84e+00 angle pdb=" N GLY A 51 " pdb=" CA GLY A 51 " pdb=" C GLY A 51 " ideal model delta sigma weight residual 111.20 114.26 -3.06 1.39e+00 5.18e-01 4.83e+00 ... (remaining 3631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 1349 15.25 - 30.50: 157 30.50 - 45.75: 36 45.75 - 61.00: 24 61.00 - 76.25: 12 Dihedral angle restraints: 1578 sinusoidal: 546 harmonic: 1032 Sorted by residual: dihedral pdb=" CA ILE F 88 " pdb=" C ILE F 88 " pdb=" N ALA F 89 " pdb=" CA ALA F 89 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ILE E 88 " pdb=" C ILE E 88 " pdb=" N ALA E 89 " pdb=" CA ALA E 89 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ILE D 88 " pdb=" C ILE D 88 " pdb=" N ALA D 89 " pdb=" CA ALA D 89 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 1575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 287 0.031 - 0.062: 91 0.062 - 0.092: 20 0.092 - 0.123: 64 0.123 - 0.154: 12 Chirality restraints: 474 Sorted by residual: chirality pdb=" CB ILE C 88 " pdb=" CA ILE C 88 " pdb=" CG1 ILE C 88 " pdb=" CG2 ILE C 88 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CB ILE E 88 " pdb=" CA ILE E 88 " pdb=" CG1 ILE E 88 " pdb=" CG2 ILE E 88 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CB ILE A 88 " pdb=" CA ILE A 88 " pdb=" CG1 ILE A 88 " pdb=" CG2 ILE A 88 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 471 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 96 " 0.005 2.00e-02 2.50e+03 9.72e-03 9.44e-01 pdb=" C LYS A 96 " -0.017 2.00e-02 2.50e+03 pdb=" O LYS A 96 " 0.006 2.00e-02 2.50e+03 pdb=" N LYS A 97 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 96 " 0.005 2.00e-02 2.50e+03 9.56e-03 9.14e-01 pdb=" C LYS C 96 " -0.017 2.00e-02 2.50e+03 pdb=" O LYS C 96 " 0.006 2.00e-02 2.50e+03 pdb=" N LYS C 97 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 96 " 0.005 2.00e-02 2.50e+03 9.52e-03 9.06e-01 pdb=" C LYS B 96 " -0.016 2.00e-02 2.50e+03 pdb=" O LYS B 96 " 0.006 2.00e-02 2.50e+03 pdb=" N LYS B 97 " 0.005 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1391 2.98 - 3.46: 2298 3.46 - 3.94: 4280 3.94 - 4.42: 4241 4.42 - 4.90: 8683 Nonbonded interactions: 20893 Sorted by model distance: nonbonded pdb=" O ALA E 89 " pdb=" N ALA F 90 " model vdw 2.503 3.120 nonbonded pdb=" O ALA B 89 " pdb=" N ALA C 90 " model vdw 2.518 3.120 nonbonded pdb=" O HIS B 50 " pdb=" OG1 THR A 72 " model vdw 2.564 3.040 nonbonded pdb=" O HIS E 50 " pdb=" OG1 THR D 72 " model vdw 2.578 3.040 nonbonded pdb=" O LYS E 60 " pdb=" N GLU F 61 " model vdw 2.589 3.120 ... (remaining 20888 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 : 0.002 0.017 2694 Z= 0.106 Angle : 0.589 4.802 3636 Z= 0.337 Chirality : 0.053 0.154 474 Planarity : 0.002 0.010 450 Dihedral : 17.480 76.250 930 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 0.00 % Allowed : 26.09 % Favored : 73.91 % 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: -2.81 (0.38), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.010 0.003 PHE C 94 TYR 0.004 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.10113 ( 16) hydrogen bonds : angle 6.43806 ( 48) covalent geometry : bond 0.00195 ( 2694) covalent geometry : angle 0.58897 ( 3636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.286 Fit side-chains REVERT: B 58 LYS cc_start: 0.7748 (mttt) cc_final: 0.7492 (tptp) REVERT: A 45 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8259 (tttm) REVERT: A 58 LYS cc_start: 0.8179 (mttt) cc_final: 0.7589 (tptp) REVERT: C 58 LYS cc_start: 0.8036 (mttt) cc_final: 0.7620 (tptp) REVERT: E 58 LYS cc_start: 0.7931 (mttt) cc_final: 0.7646 (tptp) REVERT: D 58 LYS cc_start: 0.8000 (mttt) cc_final: 0.7492 (tptp) REVERT: F 58 LYS cc_start: 0.8138 (mttt) cc_final: 0.7473 (tptp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2494 time to fit residues: 8.8373 Evaluate side-chains 31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.4797 r_free = 0.4797 target = 0.202442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.187715 restraints weight = 3647.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.191195 restraints weight = 1885.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.193581 restraints weight = 1134.323| |-----------------------------------------------------------------------------| r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2694 Z= 0.273 Angle : 0.698 5.250 3636 Z= 0.398 Chirality : 0.055 0.139 474 Planarity : 0.004 0.012 450 Dihedral : 7.554 25.124 384 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.20 % Favored : 82.80 % Rotamer: Outliers : 1.45 % Allowed : 25.00 % Favored : 73.55 % 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: -3.77 (0.31), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.24), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.003 0.002 PHE B 94 TYR 0.013 0.003 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02104 ( 16) hydrogen bonds : angle 4.12273 ( 48) covalent geometry : bond 0.00551 ( 2694) covalent geometry : angle 0.69802 ( 3636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.289 Fit side-chains REVERT: B 45 LYS cc_start: 0.8953 (tmtt) cc_final: 0.8718 (tttp) REVERT: D 34 LYS cc_start: 0.5360 (pttm) cc_final: 0.5131 (tptp) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.2674 time to fit residues: 13.1744 Evaluate side-chains 41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.229235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.218095 restraints weight = 3591.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.220879 restraints weight = 1869.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.222605 restraints weight = 1121.453| |-----------------------------------------------------------------------------| r_work (final): 0.4968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2694 Z= 0.174 Angle : 0.628 5.834 3636 Z= 0.345 Chirality : 0.052 0.164 474 Planarity : 0.002 0.007 450 Dihedral : 6.204 23.317 384 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % Rotamer: Outliers : 2.90 % Allowed : 24.64 % Favored : 72.46 % 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: -3.73 (0.31), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.23), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.001 0.000 PHE A 94 TYR 0.005 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.01564 ( 16) hydrogen bonds : angle 3.77426 ( 48) covalent geometry : bond 0.00345 ( 2694) covalent geometry : angle 0.62751 ( 3636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.272 Fit side-chains REVERT: B 58 LYS cc_start: 0.8260 (tptp) cc_final: 0.8053 (tptp) REVERT: C 58 LYS cc_start: 0.8476 (tptp) cc_final: 0.8136 (tptp) REVERT: C 75 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7599 (t) REVERT: F 75 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7687 (t) outliers start: 8 outliers final: 2 residues processed: 41 average time/residue: 0.2242 time to fit residues: 10.5134 Evaluate side-chains 38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN A 62 GLN C 62 GLN D 62 GLN F 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.192598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.178344 restraints weight = 3970.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.181493 restraints weight = 2111.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.183571 restraints weight = 1304.516| |-----------------------------------------------------------------------------| r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 2694 Z= 0.336 Angle : 0.804 7.441 3636 Z= 0.442 Chirality : 0.056 0.133 474 Planarity : 0.004 0.011 450 Dihedral : 7.537 24.803 384 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 24.46 % Favored : 75.27 % Rotamer: Outliers : 4.71 % Allowed : 24.64 % Favored : 70.65 % 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: -4.47 (0.28), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.003 0.001 PHE A 94 TYR 0.008 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.01739 ( 16) hydrogen bonds : angle 3.98982 ( 48) covalent geometry : bond 0.00676 ( 2694) covalent geometry : angle 0.80356 ( 3636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.264 Fit side-chains REVERT: B 34 LYS cc_start: 0.5319 (pttt) cc_final: 0.5066 (tttm) REVERT: B 45 LYS cc_start: 0.9040 (tttt) cc_final: 0.8813 (tttp) REVERT: A 43 LYS cc_start: 0.7889 (tttt) cc_final: 0.7624 (tttp) REVERT: A 45 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8497 (tttm) REVERT: A 58 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8117 (tptp) REVERT: C 58 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8252 (tptp) REVERT: F 43 LYS cc_start: 0.7659 (tttt) cc_final: 0.7049 (ttmt) REVERT: F 58 LYS cc_start: 0.8513 (tptp) cc_final: 0.8196 (tptp) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.2539 time to fit residues: 14.7324 Evaluate side-chains 53 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain D residue 71 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.0060 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.239707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.229429 restraints weight = 3302.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.232164 restraints weight = 1680.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.234023 restraints weight = 982.396| |-----------------------------------------------------------------------------| r_work (final): 0.5101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2694 Z= 0.096 Angle : 0.603 7.538 3636 Z= 0.315 Chirality : 0.052 0.153 474 Planarity : 0.002 0.009 450 Dihedral : 4.930 20.865 384 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.54 % Allowed : 26.81 % Favored : 70.65 % 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: -3.81 (0.30), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.23), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.003 0.001 PHE E 94 TYR 0.005 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.01474 ( 16) hydrogen bonds : angle 3.61612 ( 48) covalent geometry : bond 0.00185 ( 2694) covalent geometry : angle 0.60281 ( 3636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.271 Fit side-chains REVERT: B 45 LYS cc_start: 0.8831 (tttt) cc_final: 0.8625 (tttp) REVERT: A 45 LYS cc_start: 0.8684 (tmtt) cc_final: 0.8423 (tttm) REVERT: C 58 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8092 (tptp) REVERT: C 75 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7599 (t) REVERT: F 43 LYS cc_start: 0.7613 (tttt) cc_final: 0.7200 (ttpt) REVERT: F 58 LYS cc_start: 0.8188 (tptp) cc_final: 0.7858 (tptp) REVERT: F 75 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7594 (t) REVERT: F 83 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6958 (mm-30) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.2240 time to fit residues: 10.5379 Evaluate side-chains 40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.0040 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.219078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.209307 restraints weight = 3618.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.211581 restraints weight = 1937.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.213245 restraints weight = 1191.882| |-----------------------------------------------------------------------------| r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 2694 Z= 0.287 Angle : 0.745 8.148 3636 Z= 0.403 Chirality : 0.054 0.129 474 Planarity : 0.004 0.011 450 Dihedral : 6.795 23.479 384 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.81 % Allowed : 21.51 % Favored : 77.69 % Rotamer: Outliers : 4.35 % Allowed : 26.45 % Favored : 69.20 % 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: -4.29 (0.30), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.23), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.002 0.001 PHE A 94 TYR 0.007 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.01380 ( 16) hydrogen bonds : angle 3.78050 ( 48) covalent geometry : bond 0.00577 ( 2694) covalent geometry : angle 0.74532 ( 3636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.295 Fit side-chains REVERT: B 45 LYS cc_start: 0.8924 (tttt) cc_final: 0.8682 (tttp) REVERT: A 45 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8372 (tttm) REVERT: A 58 LYS cc_start: 0.8361 (tptp) cc_final: 0.7829 (tptp) REVERT: C 58 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8082 (tptp) REVERT: D 58 LYS cc_start: 0.8415 (tptp) cc_final: 0.8205 (tptp) REVERT: F 58 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8030 (tptp) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.2377 time to fit residues: 12.6644 Evaluate side-chains 50 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 58 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 0.0000 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.230740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.219531 restraints weight = 3520.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.222357 restraints weight = 1906.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.224207 restraints weight = 1155.554| |-----------------------------------------------------------------------------| r_work (final): 0.5009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2694 Z= 0.106 Angle : 0.606 8.635 3636 Z= 0.314 Chirality : 0.052 0.126 474 Planarity : 0.002 0.009 450 Dihedral : 4.957 21.142 384 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.99 % Allowed : 26.45 % Favored : 69.57 % 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: -3.69 (0.32), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.002 0.000 PHE B 94 TYR 0.005 0.001 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01254 ( 16) hydrogen bonds : angle 3.69667 ( 48) covalent geometry : bond 0.00208 ( 2694) covalent geometry : angle 0.60631 ( 3636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.287 Fit side-chains REVERT: B 45 LYS cc_start: 0.8854 (tttt) cc_final: 0.8499 (tttp) REVERT: B 46 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: A 45 LYS cc_start: 0.8668 (tmtt) cc_final: 0.8427 (tttm) REVERT: C 45 LYS cc_start: 0.8502 (tttt) cc_final: 0.8295 (tttt) REVERT: C 58 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7958 (tptp) REVERT: C 75 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7604 (t) REVERT: F 58 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7910 (tptp) REVERT: F 75 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7679 (t) REVERT: F 83 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6790 (mm-30) outliers start: 11 outliers final: 4 residues processed: 42 average time/residue: 0.2126 time to fit residues: 10.2834 Evaluate side-chains 44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 0.0970 chunk 32 optimal weight: 0.1980 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.224467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.213435 restraints weight = 3508.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.216064 restraints weight = 1914.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.217861 restraints weight = 1179.678| |-----------------------------------------------------------------------------| r_work (final): 0.4720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2694 Z= 0.157 Angle : 0.691 11.936 3636 Z= 0.335 Chirality : 0.052 0.125 474 Planarity : 0.002 0.010 450 Dihedral : 5.337 21.306 384 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.20 % Favored : 82.80 % Rotamer: Outliers : 4.35 % Allowed : 26.09 % Favored : 69.57 % 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: -3.68 (0.33), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.000 PHE E 94 TYR 0.005 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01206 ( 16) hydrogen bonds : angle 3.56384 ( 48) covalent geometry : bond 0.00313 ( 2694) covalent geometry : angle 0.69088 ( 3636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.260 Fit side-chains REVERT: B 45 LYS cc_start: 0.8975 (tttt) cc_final: 0.8605 (tttp) REVERT: B 46 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: A 45 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8591 (tttm) REVERT: C 58 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8046 (tptp) REVERT: C 75 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7551 (t) REVERT: F 58 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7512 (tptp) outliers start: 12 outliers final: 6 residues processed: 41 average time/residue: 0.1865 time to fit residues: 8.8808 Evaluate side-chains 44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.225344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.213916 restraints weight = 3503.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.216572 restraints weight = 1905.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.218471 restraints weight = 1175.529| |-----------------------------------------------------------------------------| r_work (final): 0.4953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2694 Z= 0.153 Angle : 0.690 11.501 3636 Z= 0.337 Chirality : 0.052 0.130 474 Planarity : 0.002 0.012 450 Dihedral : 5.309 22.255 384 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 4.71 % Allowed : 25.36 % Favored : 69.93 % 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: -3.64 (0.33), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.001 0.000 PHE B 94 TYR 0.006 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01194 ( 16) hydrogen bonds : angle 3.65443 ( 48) covalent geometry : bond 0.00305 ( 2694) covalent geometry : angle 0.68979 ( 3636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.343 Fit side-chains REVERT: B 45 LYS cc_start: 0.8901 (tttt) cc_final: 0.8555 (tttp) REVERT: B 46 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: A 45 LYS cc_start: 0.8684 (tmtt) cc_final: 0.8448 (tttm) REVERT: C 58 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8026 (tptp) REVERT: C 75 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7589 (t) REVERT: F 58 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7570 (tptp) REVERT: F 75 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7674 (t) REVERT: F 83 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7265 (mm-30) outliers start: 13 outliers final: 5 residues processed: 39 average time/residue: 0.2104 time to fit residues: 9.6592 Evaluate side-chains 45 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.231694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.220447 restraints weight = 3426.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.223103 restraints weight = 1878.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.224942 restraints weight = 1155.311| |-----------------------------------------------------------------------------| r_work (final): 0.5024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2694 Z= 0.101 Angle : 0.638 10.777 3636 Z= 0.307 Chirality : 0.052 0.138 474 Planarity : 0.002 0.013 450 Dihedral : 4.522 19.685 384 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 3.62 % Allowed : 25.72 % Favored : 70.65 % 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: -3.34 (0.35), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.002 0.000 PHE B 94 TYR 0.004 0.001 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01090 ( 16) hydrogen bonds : angle 3.51481 ( 48) covalent geometry : bond 0.00204 ( 2694) covalent geometry : angle 0.63757 ( 3636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.302 Fit side-chains REVERT: B 45 LYS cc_start: 0.8841 (tttt) cc_final: 0.8436 (tttp) REVERT: B 46 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7798 (tp30) REVERT: A 45 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8308 (tttm) REVERT: C 58 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7963 (tptp) REVERT: C 75 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7539 (t) REVERT: F 58 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7809 (tptp) REVERT: F 75 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7615 (t) outliers start: 10 outliers final: 2 residues processed: 35 average time/residue: 0.2240 time to fit residues: 9.0660 Evaluate side-chains 37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.0070 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.226213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.214977 restraints weight = 3436.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.217649 restraints weight = 1880.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.219423 restraints weight = 1158.342| |-----------------------------------------------------------------------------| r_work (final): 0.4967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2694 Z= 0.148 Angle : 0.655 10.366 3636 Z= 0.325 Chirality : 0.052 0.131 474 Planarity : 0.002 0.013 450 Dihedral : 5.112 21.135 384 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.59 % Favored : 84.41 % Rotamer: Outliers : 2.90 % Allowed : 24.64 % Favored : 72.46 % 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: -3.47 (0.35), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D 50 PHE 0.001 0.000 PHE E 94 TYR 0.005 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01149 ( 16) hydrogen bonds : angle 3.45085 ( 48) covalent geometry : bond 0.00297 ( 2694) covalent geometry : angle 0.65543 ( 3636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.09 seconds wall clock time: 23 minutes 31.07 seconds (1411.07 seconds total)