Starting phenix.real_space_refine on Wed Mar 5 15:29:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m62_23687/03_2025/7m62_23687.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m62_23687/03_2025/7m62_23687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m62_23687/03_2025/7m62_23687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m62_23687/03_2025/7m62_23687.map" model { file = "/net/cci-nas-00/data/ceres_data/7m62_23687/03_2025/7m62_23687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m62_23687/03_2025/7m62_23687.cif" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 1.000 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 10 5.16 5 C 1450 2.51 5 N 440 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2380 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 237 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.17, per 1000 atoms: 0.49 Number of scatterers: 2380 At special positions: 0 Unit cell: (68.575, 72.795, 41.145, 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 10 16.00 O 480 8.00 N 440 7.00 C 1450 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 279.3 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 37.5% 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 'G' and resid 7 through 15 removed outlier: 6.830A pdb=" N PHE D 15 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 15 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA A 8 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG F 11 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLN A 10 " --> pdb=" O ARG F 11 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA F 13 " --> pdb=" O GLN A 10 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU A 12 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE F 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 14 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA F 8 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG I 11 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN F 10 " --> pdb=" O ARG I 11 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA I 13 " --> pdb=" O GLN F 10 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU F 12 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE I 15 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN F 14 " --> pdb=" O PHE I 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 25 through 28 removed outlier: 7.002A pdb=" N SER D 28 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER A 28 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 25 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER F 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU A 27 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA F 25 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER I 28 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LEU F 27 " --> pdb=" O SER I 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 33 through 34 removed outlier: 6.760A pdb=" N GLY G 33 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY D 33 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY A 33 " --> pdb=" O SER F 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY F 33 " --> pdb=" O SER I 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 7 through 15 removed outlier: 6.831A pdb=" N PHE C 15 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE B 15 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA B 8 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG E 11 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN B 10 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA E 13 " --> pdb=" O GLN B 10 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU B 12 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE E 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN B 14 " --> pdb=" O PHE E 15 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA E 8 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG J 11 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLN E 10 " --> pdb=" O ARG J 11 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA J 13 " --> pdb=" O GLN E 10 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU E 12 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE J 15 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN E 14 " --> pdb=" O PHE J 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 25 through 28 removed outlier: 7.004A pdb=" N SER C 28 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER B 28 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA B 25 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER E 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LEU B 27 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA E 25 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER J 28 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU E 27 " --> pdb=" O SER J 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 34 removed outlier: 6.765A pdb=" N GLY H 33 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY C 33 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY B 33 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY E 33 " --> pdb=" O SER J 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 36 hydrogen bonds defined for protein. 108 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: 0.54 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 380 1.31 - 1.44: 730 1.44 - 1.56: 1280 1.56 - 1.68: 0 1.68 - 1.81: 10 Bond restraints: 2400 Sorted by residual: bond pdb=" CB ASN G 22 " pdb=" CG ASN G 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN H 22 " pdb=" CG ASN H 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN J 22 " pdb=" CG ASN J 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN I 22 " pdb=" CG ASN I 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN A 22 " pdb=" CG ASN A 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 ... (remaining 2395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 2716 1.10 - 2.20: 311 2.20 - 3.30: 133 3.30 - 4.41: 40 4.41 - 5.51: 60 Bond angle restraints: 3260 Sorted by residual: angle pdb=" N ASN F 22 " pdb=" CA ASN F 22 " pdb=" C ASN F 22 " ideal model delta sigma weight residual 109.80 114.78 -4.98 1.70e+00 3.46e-01 8.59e+00 angle pdb=" N ASN B 22 " pdb=" CA ASN B 22 " pdb=" C ASN B 22 " ideal model delta sigma weight residual 109.80 114.78 -4.98 1.70e+00 3.46e-01 8.58e+00 angle pdb=" N ASN J 22 " pdb=" CA ASN J 22 " pdb=" C ASN J 22 " ideal model delta sigma weight residual 109.80 114.77 -4.97 1.70e+00 3.46e-01 8.54e+00 angle pdb=" N ASN E 22 " pdb=" CA ASN E 22 " pdb=" C ASN E 22 " ideal model delta sigma weight residual 109.80 114.75 -4.95 1.70e+00 3.46e-01 8.49e+00 angle pdb=" N ASN D 22 " pdb=" CA ASN D 22 " pdb=" C ASN D 22 " ideal model delta sigma weight residual 109.80 114.75 -4.95 1.70e+00 3.46e-01 8.49e+00 ... (remaining 3255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.29: 1110 11.29 - 22.58: 160 22.58 - 33.87: 70 33.87 - 45.17: 30 45.17 - 56.46: 10 Dihedral angle restraints: 1380 sinusoidal: 460 harmonic: 920 Sorted by residual: dihedral pdb=" CA ASN I 21 " pdb=" C ASN I 21 " pdb=" N ASN I 22 " pdb=" CA ASN I 22 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ASN G 21 " pdb=" C ASN G 21 " pdb=" N ASN G 22 " pdb=" CA ASN G 22 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASN A 21 " pdb=" C ASN A 21 " pdb=" N ASN A 22 " pdb=" CA ASN A 22 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 1377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 299 0.059 - 0.118: 71 0.118 - 0.177: 10 0.177 - 0.236: 10 0.236 - 0.295: 10 Chirality restraints: 400 Sorted by residual: chirality pdb=" CB ILE H 26 " pdb=" CA ILE H 26 " pdb=" CG1 ILE H 26 " pdb=" CG2 ILE H 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE C 26 " pdb=" CA ILE C 26 " pdb=" CG1 ILE C 26 " pdb=" CG2 ILE C 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB ILE D 26 " pdb=" CA ILE D 26 " pdb=" CG1 ILE D 26 " pdb=" CG2 ILE D 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 397 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 20 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C SER D 20 " 0.020 2.00e-02 2.50e+03 pdb=" O SER D 20 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN D 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 20 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C SER H 20 " 0.020 2.00e-02 2.50e+03 pdb=" O SER H 20 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN H 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 20 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C SER C 20 " -0.020 2.00e-02 2.50e+03 pdb=" O SER C 20 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 21 " 0.007 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 772 2.84 - 3.35: 2438 3.35 - 3.87: 4244 3.87 - 4.38: 4566 4.38 - 4.90: 9080 Nonbonded interactions: 21100 Sorted by model distance: nonbonded pdb=" O ASN A 22 " pdb=" N NH2 D 38 " model vdw 2.321 3.120 nonbonded pdb=" N NH2 B 38 " pdb=" O ASN E 22 " model vdw 2.321 3.120 nonbonded pdb=" O ASN C 22 " pdb=" N NH2 H 38 " model vdw 2.321 3.120 nonbonded pdb=" N NH2 F 38 " pdb=" O ASN I 22 " model vdw 2.321 3.120 nonbonded pdb=" O ASN B 22 " pdb=" N NH2 C 38 " model vdw 2.325 3.120 ... (remaining 21095 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.090 Find NCS groups from input model: 0.140 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 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 : 0.007 0.079 2400 Z= 0.502 Angle : 1.134 5.506 3260 Z= 0.654 Chirality : 0.073 0.295 400 Planarity : 0.003 0.011 420 Dihedral : 14.835 56.457 780 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -4.97 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 18 PHE 0.008 0.003 PHE D 23 TYR 0.003 0.001 TYR H 37 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.277 Fit side-chains REVERT: A 14 ASN cc_start: 0.8754 (t0) cc_final: 0.8460 (t0) REVERT: B 14 ASN cc_start: 0.8716 (t0) cc_final: 0.8419 (t0) REVERT: C 14 ASN cc_start: 0.8789 (t0) cc_final: 0.8472 (t0) REVERT: D 14 ASN cc_start: 0.8791 (t0) cc_final: 0.8472 (t0) REVERT: E 14 ASN cc_start: 0.8779 (t0) cc_final: 0.8464 (t0) REVERT: F 14 ASN cc_start: 0.8778 (t0) cc_final: 0.8458 (t0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2969 time to fit residues: 13.1152 Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 50.0000 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 21 ASN B 14 ASN B 21 ASN C 14 ASN C 21 ASN D 14 ASN D 21 ASN E 14 ASN E 21 ASN F 14 ASN F 21 ASN G 21 ASN H 21 ASN I 21 ASN J 21 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.110665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.101244 restraints weight = 9523.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.103955 restraints weight = 5241.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.105919 restraints weight = 3277.140| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2400 Z= 0.322 Angle : 1.008 7.786 3260 Z= 0.555 Chirality : 0.057 0.210 400 Planarity : 0.004 0.019 420 Dihedral : 12.317 35.162 330 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 2.22 % Allowed : 18.52 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.87 % 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: -4.59 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.022 0.003 PHE E 23 TYR 0.009 0.002 TYR H 37 ARG 0.005 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.268 Fit side-chains REVERT: C 14 ASN cc_start: 0.8642 (t0) cc_final: 0.8224 (t0) REVERT: D 14 ASN cc_start: 0.8701 (t0) cc_final: 0.8254 (t0) REVERT: F 14 ASN cc_start: 0.8984 (t0) cc_final: 0.8742 (t0) REVERT: G 11 ARG cc_start: 0.4259 (pmt-80) cc_final: 0.3205 (mmm160) REVERT: H 11 ARG cc_start: 0.4406 (pmt-80) cc_final: 0.3221 (mmm160) outliers start: 6 outliers final: 2 residues processed: 18 average time/residue: 0.1705 time to fit residues: 3.8369 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 22 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 50.0000 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 19 optimal weight: 40.0000 chunk 12 optimal weight: 30.0000 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 70.0000 chunk 10 optimal weight: 20.0000 overall best weight: 11.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN D 14 ASN G 14 ASN H 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.121343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.111977 restraints weight = 10335.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.113921 restraints weight = 5718.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.115003 restraints weight = 3543.553| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2400 Z= 0.376 Angle : 1.047 8.108 3260 Z= 0.568 Chirality : 0.061 0.380 400 Planarity : 0.003 0.019 420 Dihedral : 12.560 36.624 330 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 27.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.67 % Favored : 79.33 % Rotamer: Outliers : 8.89 % Allowed : 16.30 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.52 % 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: -4.37 (0.40), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.013 0.003 PHE A 23 TYR 0.009 0.002 TYR H 37 ARG 0.002 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 18 time to evaluate : 0.296 Fit side-chains REVERT: G 11 ARG cc_start: 0.4532 (pmt-80) cc_final: 0.3286 (pmt-80) REVERT: H 11 ARG cc_start: 0.4564 (pmt-80) cc_final: 0.3322 (pmt-80) outliers start: 24 outliers final: 16 residues processed: 42 average time/residue: 0.1117 time to fit residues: 6.0101 Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 18 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 32 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 0 optimal weight: 70.0000 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 50.0000 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.4545 r_free = 0.4545 target = 0.128998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.118780 restraints weight = 10331.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.120793 restraints weight = 5689.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.122002 restraints weight = 3503.296| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2400 Z= 0.255 Angle : 0.964 7.736 3260 Z= 0.525 Chirality : 0.062 0.387 400 Planarity : 0.003 0.011 420 Dihedral : 12.253 33.258 330 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.67 % Favored : 80.33 % Rotamer: Outliers : 7.41 % Allowed : 16.30 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % 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: -4.38 (0.40), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.010 0.003 PHE A 23 TYR 0.005 0.001 TYR G 37 ARG 0.002 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.290 Fit side-chains REVERT: C 14 ASN cc_start: 0.9020 (t0) cc_final: 0.8808 (t0) REVERT: G 11 ARG cc_start: 0.4676 (pmt-80) cc_final: 0.3730 (pmt-80) REVERT: H 11 ARG cc_start: 0.4671 (pmt-80) cc_final: 0.3723 (pmt-80) outliers start: 20 outliers final: 14 residues processed: 38 average time/residue: 0.1084 time to fit residues: 5.3063 Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain J residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 80.0000 chunk 28 optimal weight: 50.0000 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 29 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 ASN G 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.127307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.117384 restraints weight = 10490.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.119039 restraints weight = 5571.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.120357 restraints weight = 3529.630| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2400 Z= 0.266 Angle : 0.978 7.426 3260 Z= 0.527 Chirality : 0.064 0.446 400 Planarity : 0.003 0.011 420 Dihedral : 12.076 31.908 330 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.67 % Favored : 79.33 % Rotamer: Outliers : 8.15 % Allowed : 17.04 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % 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: -4.40 (0.39), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.011 0.002 PHE B 23 TYR 0.006 0.001 TYR G 37 ARG 0.001 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 19 time to evaluate : 0.315 Fit side-chains REVERT: H 11 ARG cc_start: 0.4940 (pmt-80) cc_final: 0.3805 (pmt-80) outliers start: 22 outliers final: 20 residues processed: 40 average time/residue: 0.0847 time to fit residues: 4.6437 Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 17 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain J residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.133063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.122886 restraints weight = 10394.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.124573 restraints weight = 5509.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.125816 restraints weight = 3507.039| |-----------------------------------------------------------------------------| r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2400 Z= 0.224 Angle : 0.951 7.376 3260 Z= 0.514 Chirality : 0.062 0.432 400 Planarity : 0.003 0.011 420 Dihedral : 11.871 32.007 330 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Rotamer: Outliers : 10.00 % Allowed : 16.30 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.29 % 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: -4.44 (0.39), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.011 0.002 PHE A 23 TYR 0.003 0.001 TYR H 37 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 21 time to evaluate : 0.283 Fit side-chains outliers start: 27 outliers final: 20 residues processed: 44 average time/residue: 0.0559 time to fit residues: 3.7291 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 21 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 9 optimal weight: 50.0000 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 0.0000 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 0.0470 chunk 18 optimal weight: 20.0000 overall best weight: 4.2088 ------------------------------------------------------------------------------- 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 = 0.4647 r_free = 0.4647 target = 0.132129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.125560 restraints weight = 8443.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.127714 restraints weight = 4590.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.129035 restraints weight = 2783.822| |-----------------------------------------------------------------------------| r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2400 Z= 0.196 Angle : 0.917 7.113 3260 Z= 0.494 Chirality : 0.059 0.424 400 Planarity : 0.002 0.010 420 Dihedral : 11.429 29.891 330 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.67 % Favored : 82.33 % Rotamer: Outliers : 7.41 % Allowed : 20.00 % Favored : 72.59 % 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: -4.66 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 18 PHE 0.013 0.002 PHE A 23 TYR 0.002 0.001 TYR H 37 ARG 0.001 0.000 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 21 time to evaluate : 0.291 Fit side-chains REVERT: C 26 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6782 (pt) REVERT: D 26 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.6891 (pt) REVERT: H 11 ARG cc_start: 0.4957 (pmt-80) cc_final: 0.3892 (pmt-80) outliers start: 20 outliers final: 13 residues processed: 39 average time/residue: 0.0863 time to fit residues: 4.6609 Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.133749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.121956 restraints weight = 10924.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.123866 restraints weight = 6035.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.125241 restraints weight = 3919.877| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2400 Z= 0.269 Angle : 0.971 7.549 3260 Z= 0.520 Chirality : 0.061 0.502 400 Planarity : 0.003 0.012 420 Dihedral : 11.656 31.586 330 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.67 % Favored : 77.33 % Rotamer: Outliers : 9.63 % Allowed : 18.52 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.29 % 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: -4.51 (0.39), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.009 0.002 PHE B 23 TYR 0.005 0.001 TYR H 37 ARG 0.001 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 22 time to evaluate : 0.264 Fit side-chains REVERT: C 26 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7019 (pt) REVERT: D 26 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7005 (pt) REVERT: G 11 ARG cc_start: 0.4948 (pmt-80) cc_final: 0.4092 (pmt-80) REVERT: H 11 ARG cc_start: 0.4971 (pmt-80) cc_final: 0.4068 (pmt-80) outliers start: 26 outliers final: 20 residues processed: 44 average time/residue: 0.1015 time to fit residues: 5.7792 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 22 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 30.0000 chunk 0 optimal weight: 70.0000 chunk 16 optimal weight: 40.0000 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.128261 restraints weight = 10558.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.130325 restraints weight = 5914.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.131524 restraints weight = 3762.789| |-----------------------------------------------------------------------------| r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2400 Z= 0.190 Angle : 0.921 7.357 3260 Z= 0.496 Chirality : 0.058 0.470 400 Planarity : 0.003 0.016 420 Dihedral : 11.356 31.049 330 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.33 % Favored : 83.67 % Rotamer: Outliers : 7.78 % Allowed : 20.37 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.29 % 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: -4.73 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 18 PHE 0.012 0.002 PHE A 23 TYR 0.003 0.001 TYR H 37 ARG 0.001 0.000 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 19 time to evaluate : 0.292 Fit side-chains REVERT: C 26 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6763 (pt) REVERT: D 26 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6791 (pt) REVERT: G 11 ARG cc_start: 0.4988 (pmt-80) cc_final: 0.3938 (pmt-80) REVERT: H 11 ARG cc_start: 0.4995 (pmt-80) cc_final: 0.3942 (pmt-80) outliers start: 21 outliers final: 13 residues processed: 37 average time/residue: 0.1162 time to fit residues: 5.4781 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 18 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 50.0000 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 25 optimal weight: 0.0270 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 0.0570 overall best weight: 5.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.138472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.126312 restraints weight = 10601.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.128160 restraints weight = 5869.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.129302 restraints weight = 3710.186| |-----------------------------------------------------------------------------| r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2400 Z= 0.216 Angle : 0.929 7.175 3260 Z= 0.501 Chirality : 0.058 0.474 400 Planarity : 0.003 0.018 420 Dihedral : 11.288 31.058 330 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.33 % Favored : 77.67 % Rotamer: Outliers : 5.93 % Allowed : 22.59 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.29 % 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: -4.88 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.009 0.002 PHE B 23 TYR 0.003 0.001 TYR D 37 ARG 0.002 0.000 ARG H 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 18 time to evaluate : 0.258 Fit side-chains REVERT: C 26 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6832 (pt) REVERT: D 26 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6838 (pt) REVERT: E 26 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8668 (tt) REVERT: G 11 ARG cc_start: 0.5022 (pmt-80) cc_final: 0.4084 (pmt-80) REVERT: H 11 ARG cc_start: 0.5105 (pmt-80) cc_final: 0.4098 (pmt-80) outliers start: 16 outliers final: 9 residues processed: 31 average time/residue: 0.1174 time to fit residues: 4.5968 Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 21 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 70.0000 chunk 6 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN D 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.142048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.128738 restraints weight = 10605.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.130803 restraints weight = 6008.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.132172 restraints weight = 3827.006| |-----------------------------------------------------------------------------| r_work (final): 0.4646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2400 Z= 0.194 Angle : 0.918 7.370 3260 Z= 0.495 Chirality : 0.058 0.463 400 Planarity : 0.003 0.020 420 Dihedral : 11.147 31.294 330 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.33 % Favored : 80.67 % Rotamer: Outliers : 5.93 % Allowed : 21.85 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.29 % 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: -4.97 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 18 PHE 0.011 0.002 PHE B 23 TYR 0.003 0.001 TYR C 37 ARG 0.002 0.000 ARG H 11 =============================================================================== Job complete usr+sys time: 925.52 seconds wall clock time: 17 minutes 12.90 seconds (1032.90 seconds total)