Starting phenix.real_space_refine on Tue Mar 3 10:57:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m62_23687/03_2026/7m62_23687.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m62_23687/03_2026/7m62_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_2026/7m62_23687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m62_23687/03_2026/7m62_23687.map" model { file = "/net/cci-nas-00/data/ceres_data/7m62_23687/03_2026/7m62_23687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m62_23687/03_2026/7m62_23687.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.39, per 1000 atoms: 0.16 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: 0.24 Conformation dependent library (CDL) restraints added in 74.6 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: 0.09 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: 0.34 Time building geometry restraints manager: 0.32 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.680 ------------------------------------------------------------------------------- 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 : 0.010 0.102 2410 Z= 0.728 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.001 0.000 ARG B 11 TYR 0.003 0.001 TYR H 37 PHE 0.008 0.003 PHE D 23 HIS 0.001 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00734 ( 2400) covalent geometry : angle 1.13445 ( 3260) hydrogen bonds : bond 0.26524 ( 36) hydrogen bonds : angle 14.24915 ( 108) Misc. bond : bond 0.10138 ( 10) *********************** 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 : 0.096 Fit side-chains REVERT: A 14 ASN cc_start: 0.8754 (t0) cc_final: 0.8461 (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: 0.8792 (t0) cc_final: 0.8473 (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: 0.1314 time to fit residues: 5.7419 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 : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.111886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.102381 restraints weight = 9336.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.105123 restraints weight = 5176.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.107154 restraints weight = 3256.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.108535 restraints weight = 2154.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.109572 restraints weight = 1415.534| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 2410 Z= 0.199 Angle : 0.996 7.533 3260 Z= 0.552 Chirality : 0.057 0.221 400 Planarity : 0.004 0.016 420 Dihedral : 12.305 35.444 330 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.33 % Favored : 80.67 % Rotamer: Outliers : 2.22 % Allowed : 18.89 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.87 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG C 11 TYR 0.010 0.002 TYR I 37 PHE 0.023 0.003 PHE E 23 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 2400) covalent geometry : angle 0.99611 ( 3260) hydrogen bonds : bond 0.04328 ( 36) hydrogen bonds : angle 7.97823 ( 108) Misc. bond : bond 0.00016 ( 10) *********************** 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 : 0.095 Fit side-chains REVERT: C 14 ASN cc_start: 0.8685 (t0) cc_final: 0.8260 (t0) REVERT: D 14 ASN cc_start: 0.8668 (t0) cc_final: 0.8243 (t0) REVERT: G 11 ARG cc_start: 0.4305 (pmt-80) cc_final: 0.3201 (mmm160) REVERT: H 11 ARG cc_start: 0.4261 (pmt-80) cc_final: 0.3210 (mmm160) outliers start: 6 outliers final: 2 residues processed: 18 average time/residue: 0.0733 time to fit residues: 1.6315 Evaluate side-chains 14 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.069 ------------------------------------------------------------------------------- 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 5 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 40.0000 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.4535 r_free = 0.4535 target = 0.129829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.119063 restraints weight = 10540.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.121253 restraints weight = 5939.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.122603 restraints weight = 3731.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.123540 restraints weight = 2573.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.123895 restraints weight = 1822.507| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2410 Z= 0.162 Angle : 0.948 7.208 3260 Z= 0.515 Chirality : 0.056 0.337 400 Planarity : 0.003 0.014 420 Dihedral : 12.032 34.072 330 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.67 % Favored : 78.33 % Rotamer: Outliers : 5.93 % Allowed : 17.04 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.38), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 11 TYR 0.005 0.001 TYR H 37 PHE 0.011 0.002 PHE A 23 HIS 0.001 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 2400) covalent geometry : angle 0.94775 ( 3260) hydrogen bonds : bond 0.04787 ( 36) hydrogen bonds : angle 7.81167 ( 108) Misc. bond : bond 0.00019 ( 10) *********************** 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 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 14 time to evaluate : 0.099 Fit side-chains REVERT: C 14 ASN cc_start: 0.8920 (t0) cc_final: 0.8328 (t0) REVERT: D 14 ASN cc_start: 0.8840 (t0) cc_final: 0.8289 (t0) REVERT: G 11 ARG cc_start: 0.3821 (pmt-80) cc_final: 0.2792 (pmt-80) REVERT: H 11 ARG cc_start: 0.3833 (pmt-80) cc_final: 0.2767 (pmt-80) REVERT: J 14 ASN cc_start: 0.8587 (t0) cc_final: 0.8383 (t0) outliers start: 16 outliers final: 8 residues processed: 28 average time/residue: 0.0645 time to fit residues: 2.2428 Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 50.0000 chunk 25 optimal weight: 30.0000 chunk 4 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 0.0570 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.134239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.123388 restraints weight = 10670.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.125538 restraints weight = 5972.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.127026 restraints weight = 3768.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.127882 restraints weight = 2543.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.128539 restraints weight = 1858.537| |-----------------------------------------------------------------------------| r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2410 Z= 0.136 Angle : 0.936 7.255 3260 Z= 0.506 Chirality : 0.059 0.353 400 Planarity : 0.002 0.009 420 Dihedral : 11.629 30.705 330 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.33 % Favored : 79.67 % Rotamer: Outliers : 7.41 % Allowed : 15.56 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 11 TYR 0.004 0.001 TYR G 37 PHE 0.010 0.002 PHE B 23 HIS 0.001 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2400) covalent geometry : angle 0.93622 ( 3260) hydrogen bonds : bond 0.03523 ( 36) hydrogen bonds : angle 7.22387 ( 108) Misc. bond : bond 0.00011 ( 10) *********************** 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 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 20 time to evaluate : 0.099 Fit side-chains REVERT: C 14 ASN cc_start: 0.8791 (t0) cc_final: 0.8313 (t0) REVERT: D 14 ASN cc_start: 0.8795 (t0) cc_final: 0.8301 (t0) REVERT: G 11 ARG cc_start: 0.4126 (pmt-80) cc_final: 0.2706 (pmt-80) REVERT: H 11 ARG cc_start: 0.4127 (pmt-80) cc_final: 0.2683 (pmt-80) outliers start: 20 outliers final: 12 residues processed: 40 average time/residue: 0.0546 time to fit residues: 2.7318 Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 16 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 30 THR 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 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 28 optimal weight: 0.0980 chunk 22 optimal weight: 0.0570 chunk 4 optimal weight: 40.0000 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 40.0000 chunk 15 optimal weight: 30.0000 chunk 17 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.8304 ------------------------------------------------------------------------------- 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 = 0.4644 r_free = 0.4644 target = 0.137649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.125985 restraints weight = 10347.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.128088 restraints weight = 5790.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.129475 restraints weight = 3631.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.130301 restraints weight = 2445.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.130941 restraints weight = 1815.300| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2410 Z= 0.133 Angle : 0.920 7.023 3260 Z= 0.491 Chirality : 0.058 0.452 400 Planarity : 0.002 0.012 420 Dihedral : 11.449 31.165 330 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 8.89 % Allowed : 15.56 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.39), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 11 TYR 0.003 0.001 TYR H 37 PHE 0.010 0.002 PHE A 23 HIS 0.001 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2400) covalent geometry : angle 0.91995 ( 3260) hydrogen bonds : bond 0.03827 ( 36) hydrogen bonds : angle 7.16067 ( 108) Misc. bond : bond 0.00012 ( 10) *********************** 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 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 20 time to evaluate : 0.096 Fit side-chains REVERT: C 14 ASN cc_start: 0.8786 (t0) cc_final: 0.8464 (t0) REVERT: D 14 ASN cc_start: 0.8741 (t0) cc_final: 0.8444 (t0) REVERT: G 11 ARG cc_start: 0.4585 (pmt-80) cc_final: 0.3462 (pmt-80) REVERT: H 11 ARG cc_start: 0.4582 (pmt-80) cc_final: 0.3451 (pmt-80) REVERT: I 14 ASN cc_start: 0.8831 (t0) cc_final: 0.8625 (t0) outliers start: 24 outliers final: 15 residues processed: 42 average time/residue: 0.0444 time to fit residues: 2.3359 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 : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 VAL 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 22 ASN 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 22 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 40.0000 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 10 optimal weight: 9.9990 overall best weight: 1.5954 ------------------------------------------------------------------------------- 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 = 0.4700 r_free = 0.4700 target = 0.137127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.128725 restraints weight = 8576.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.131125 restraints weight = 5012.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.132812 restraints weight = 3221.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.133977 restraints weight = 2171.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.134827 restraints weight = 1499.996| |-----------------------------------------------------------------------------| r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2410 Z= 0.104 Angle : 0.879 6.876 3260 Z= 0.467 Chirality : 0.055 0.409 400 Planarity : 0.002 0.010 420 Dihedral : 10.912 29.037 330 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.44 % Allowed : 20.00 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 11 TYR 0.002 0.000 TYR J 37 PHE 0.009 0.002 PHE A 23 HIS 0.001 0.000 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 2400) covalent geometry : angle 0.87891 ( 3260) hydrogen bonds : bond 0.02940 ( 36) hydrogen bonds : angle 6.47413 ( 108) Misc. bond : bond 0.00010 ( 10) *********************** 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 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.096 Fit side-chains REVERT: C 14 ASN cc_start: 0.8948 (t0) cc_final: 0.8467 (t0) REVERT: C 26 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6844 (pt) REVERT: D 14 ASN cc_start: 0.8957 (t0) cc_final: 0.8523 (t0) REVERT: D 26 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6852 (pt) REVERT: E 14 ASN cc_start: 0.8921 (t0) cc_final: 0.8360 (t0) REVERT: F 14 ASN cc_start: 0.8929 (t0) cc_final: 0.8400 (t0) REVERT: G 11 ARG cc_start: 0.3985 (pmt-80) cc_final: 0.2960 (pmt-80) REVERT: H 11 ARG cc_start: 0.3952 (pmt-80) cc_final: 0.2918 (pmt-80) outliers start: 12 outliers final: 6 residues processed: 32 average time/residue: 0.0457 time to fit residues: 1.8553 Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 ILE Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 0.0040 chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 5.2598 ------------------------------------------------------------------------------- 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 = 0.4724 r_free = 0.4724 target = 0.142149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.129854 restraints weight = 10343.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.131929 restraints weight = 5910.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.133150 restraints weight = 3806.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.134217 restraints weight = 2773.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.134832 restraints weight = 1996.018| |-----------------------------------------------------------------------------| r_work (final): 0.4678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2410 Z= 0.135 Angle : 0.948 8.426 3260 Z= 0.486 Chirality : 0.057 0.441 400 Planarity : 0.002 0.010 420 Dihedral : 10.973 29.880 330 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.33 % Favored : 78.67 % Rotamer: Outliers : 5.93 % Allowed : 19.63 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.38), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 11 TYR 0.003 0.001 TYR G 37 PHE 0.007 0.002 PHE J 23 HIS 0.001 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2400) covalent geometry : angle 0.94769 ( 3260) hydrogen bonds : bond 0.03440 ( 36) hydrogen bonds : angle 6.71739 ( 108) Misc. bond : bond 0.00015 ( 10) *********************** 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 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 20 time to evaluate : 0.091 Fit side-chains REVERT: C 14 ASN cc_start: 0.8917 (t0) cc_final: 0.8414 (t0) REVERT: C 26 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6824 (pt) REVERT: D 14 ASN cc_start: 0.8886 (t0) cc_final: 0.8380 (t0) REVERT: D 26 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6807 (pt) REVERT: F 14 ASN cc_start: 0.8795 (t0) cc_final: 0.8462 (t0) REVERT: G 11 ARG cc_start: 0.4497 (pmt-80) cc_final: 0.3390 (pmt-80) REVERT: H 11 ARG cc_start: 0.4457 (pmt-80) cc_final: 0.3376 (pmt-80) outliers start: 16 outliers final: 12 residues processed: 34 average time/residue: 0.0457 time to fit residues: 1.9509 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 : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 26 ILE 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 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 32 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4720 r_free = 0.4720 target = 0.141084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.129450 restraints weight = 10462.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.131461 restraints weight = 5678.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.132740 restraints weight = 3533.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.133583 restraints weight = 2408.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.134137 restraints weight = 1760.493| |-----------------------------------------------------------------------------| r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2410 Z= 0.139 Angle : 0.959 7.421 3260 Z= 0.495 Chirality : 0.058 0.458 400 Planarity : 0.003 0.012 420 Dihedral : 11.098 30.276 330 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 5.93 % Allowed : 20.00 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.38), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 11 TYR 0.004 0.001 TYR H 37 PHE 0.007 0.002 PHE A 15 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2400) covalent geometry : angle 0.95943 ( 3260) hydrogen bonds : bond 0.03327 ( 36) hydrogen bonds : angle 6.74375 ( 108) Misc. bond : bond 0.00019 ( 10) *********************** 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 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.090 Fit side-chains REVERT: C 14 ASN cc_start: 0.8901 (t0) cc_final: 0.8359 (t0) REVERT: C 26 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6827 (pt) REVERT: D 14 ASN cc_start: 0.8928 (t0) cc_final: 0.8348 (t0) REVERT: D 26 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6832 (pt) REVERT: G 11 ARG cc_start: 0.4654 (pmt-80) cc_final: 0.3647 (pmt-80) REVERT: H 11 ARG cc_start: 0.4663 (pmt-80) cc_final: 0.3546 (pmt-80) outliers start: 16 outliers final: 10 residues processed: 31 average time/residue: 0.0393 time to fit residues: 1.5926 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 : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 chunk 9 optimal weight: 40.0000 chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4729 r_free = 0.4729 target = 0.143230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.130088 restraints weight = 10845.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.131926 restraints weight = 6032.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.133428 restraints weight = 4073.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.134360 restraints weight = 2762.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.135008 restraints weight = 2053.157| |-----------------------------------------------------------------------------| r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2410 Z= 0.121 Angle : 0.948 7.529 3260 Z= 0.486 Chirality : 0.058 0.465 400 Planarity : 0.002 0.010 420 Dihedral : 10.874 30.320 330 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.67 % Favored : 81.33 % Rotamer: Outliers : 5.19 % Allowed : 20.37 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.39), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 TYR 0.003 0.001 TYR G 37 PHE 0.008 0.002 PHE D 23 HIS 0.001 0.000 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2400) covalent geometry : angle 0.94783 ( 3260) hydrogen bonds : bond 0.03104 ( 36) hydrogen bonds : angle 6.53135 ( 108) Misc. bond : bond 0.00009 ( 10) *********************** 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 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.054 Fit side-chains REVERT: C 14 ASN cc_start: 0.8785 (t0) cc_final: 0.8228 (t0) REVERT: C 26 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6709 (pt) REVERT: D 14 ASN cc_start: 0.8811 (t0) cc_final: 0.8248 (t0) REVERT: D 26 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6744 (pt) REVERT: E 14 ASN cc_start: 0.8828 (t0) cc_final: 0.8449 (t0) REVERT: G 11 ARG cc_start: 0.4693 (pmt-80) cc_final: 0.3649 (pmt-80) REVERT: H 11 ARG cc_start: 0.4670 (pmt-80) cc_final: 0.3623 (pmt-80) outliers start: 14 outliers final: 6 residues processed: 30 average time/residue: 0.0361 time to fit residues: 1.3637 Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.0170 chunk 3 optimal weight: 50.0000 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 70.0000 overall best weight: 4.4026 ------------------------------------------------------------------------------- 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 = 0.4752 r_free = 0.4752 target = 0.144551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.131130 restraints weight = 10745.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.133239 restraints weight = 6153.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.134482 restraints weight = 3996.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.135535 restraints weight = 2905.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.136087 restraints weight = 2108.573| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2410 Z= 0.125 Angle : 0.952 7.402 3260 Z= 0.488 Chirality : 0.062 0.527 400 Planarity : 0.002 0.012 420 Dihedral : 10.830 29.485 330 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.67 % Favored : 80.33 % Rotamer: Outliers : 4.44 % Allowed : 21.11 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 11 TYR 0.003 0.001 TYR G 37 PHE 0.008 0.002 PHE F 15 HIS 0.001 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2400) covalent geometry : angle 0.95191 ( 3260) hydrogen bonds : bond 0.03133 ( 36) hydrogen bonds : angle 6.71676 ( 108) Misc. bond : bond 0.00011 ( 10) ********************** 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 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.077 Fit side-chains REVERT: C 14 ASN cc_start: 0.8801 (t0) cc_final: 0.8215 (t0) REVERT: D 14 ASN cc_start: 0.8669 (t0) cc_final: 0.8140 (t0) REVERT: E 14 ASN cc_start: 0.8838 (t0) cc_final: 0.8375 (t0) REVERT: F 14 ASN cc_start: 0.8874 (t0) cc_final: 0.8482 (t0) REVERT: G 11 ARG cc_start: 0.4722 (pmt-80) cc_final: 0.3616 (pmt-80) REVERT: H 11 ARG cc_start: 0.4784 (pmt-80) cc_final: 0.3626 (pmt-80) outliers start: 12 outliers final: 4 residues processed: 29 average time/residue: 0.0549 time to fit residues: 1.9403 Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 0.0040 chunk 11 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 overall best weight: 5.8000 ------------------------------------------------------------------------------- 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 = 0.4747 r_free = 0.4747 target = 0.143587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.129891 restraints weight = 10779.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.131635 restraints weight = 6137.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.133152 restraints weight = 4192.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.134227 restraints weight = 2954.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.134773 restraints weight = 2185.168| |-----------------------------------------------------------------------------| r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2410 Z= 0.144 Angle : 0.949 8.483 3260 Z= 0.492 Chirality : 0.049 0.248 400 Planarity : 0.003 0.012 420 Dihedral : 10.786 30.099 330 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.33 % Favored : 78.67 % Rotamer: Outliers : 1.48 % Allowed : 22.96 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.38), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 11 TYR 0.004 0.001 TYR G 37 PHE 0.007 0.001 PHE J 23 HIS 0.001 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2400) covalent geometry : angle 0.94905 ( 3260) hydrogen bonds : bond 0.02797 ( 36) hydrogen bonds : angle 7.10919 ( 108) Misc. bond : bond 0.00015 ( 10) =============================================================================== Job complete usr+sys time: 492.10 seconds wall clock time: 9 minutes 13.78 seconds (553.78 seconds total)