Starting phenix.real_space_refine on Tue Feb 3 12:57:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jc5_61357/02_2026/9jc5_61357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jc5_61357/02_2026/9jc5_61357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jc5_61357/02_2026/9jc5_61357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jc5_61357/02_2026/9jc5_61357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jc5_61357/02_2026/9jc5_61357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jc5_61357/02_2026/9jc5_61357.map" } resolution = 3.23 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1647 2.51 5 N 450 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2637 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 435 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 444 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: C, E, D, F Time building chain proxies: 0.45, per 1000 atoms: 0.17 Number of scatterers: 2637 At special positions: 0 Unit cell: (81.34, 112.05, 34.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 540 8.00 N 450 7.00 C 1647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 104.6 milliseconds 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 654 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.718A pdb=" N LEU C 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.328A pdb=" N VAL A 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.531A pdb=" N THR C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA E 56 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.520A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.751A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.318A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 94 through 95 removed outlier: 6.532A pdb=" N PHE A 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.387A pdb=" N LEU D 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.438A pdb=" N VAL B 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.450A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.514A pdb=" N VAL B 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.740A pdb=" N THR D 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.532A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 95 through 96 removed outlier: 6.538A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) 21 hydrogen bonds defined for protein. 63 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: 0.20 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 468 1.28 - 1.35: 402 1.35 - 1.41: 98 1.41 - 1.48: 439 1.48 - 1.54: 1242 Bond restraints: 2649 Sorted by residual: bond pdb=" CA GLN E 79 " pdb=" CB GLN E 79 " ideal model delta sigma weight residual 1.535 1.514 0.021 1.71e-02 3.42e+03 1.57e+00 bond pdb=" CA GLN A 79 " pdb=" CB GLN A 79 " ideal model delta sigma weight residual 1.535 1.515 0.021 1.71e-02 3.42e+03 1.47e+00 bond pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " ideal model delta sigma weight residual 1.535 1.515 0.021 1.71e-02 3.42e+03 1.44e+00 bond pdb=" CG GLN E 79 " pdb=" CD GLN E 79 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CG GLN C 79 " pdb=" CD GLN C 79 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.06e+00 ... (remaining 2644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 3146 1.09 - 2.17: 363 2.17 - 3.26: 55 3.26 - 4.34: 12 4.34 - 5.43: 12 Bond angle restraints: 3588 Sorted by residual: angle pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta sigma weight residual 121.80 116.88 4.92 1.71e+00 3.42e-01 8.27e+00 angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 121.80 116.92 4.88 1.71e+00 3.42e-01 8.16e+00 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.80 116.93 4.87 1.71e+00 3.42e-01 8.13e+00 angle pdb=" OG1 THR C 59 " pdb=" CB THR C 59 " pdb=" CG2 THR C 59 " ideal model delta sigma weight residual 109.30 103.87 5.43 2.00e+00 2.50e-01 7.37e+00 angle pdb=" OG1 THR E 59 " pdb=" CB THR E 59 " pdb=" CG2 THR E 59 " ideal model delta sigma weight residual 109.30 103.88 5.42 2.00e+00 2.50e-01 7.34e+00 ... (remaining 3583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 1387 13.92 - 27.83: 110 27.83 - 41.74: 36 41.74 - 55.66: 18 55.66 - 69.57: 9 Dihedral angle restraints: 1560 sinusoidal: 531 harmonic: 1029 Sorted by residual: dihedral pdb=" CA GLU F 61 " pdb=" C GLU F 61 " pdb=" N GLN F 62 " pdb=" CA GLN F 62 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLU B 61 " pdb=" C GLU B 61 " pdb=" N GLN B 62 " pdb=" CA GLN B 62 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLU D 61 " pdb=" C GLU D 61 " pdb=" N GLN D 62 " pdb=" CA GLN D 62 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 219 0.034 - 0.067: 147 0.067 - 0.101: 63 0.101 - 0.134: 39 0.134 - 0.168: 9 Chirality restraints: 477 Sorted by residual: chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 474 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.011 2.00e-02 2.50e+03 8.93e-03 1.20e+00 pdb=" CG HIS A 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " 0.011 2.00e-02 2.50e+03 8.90e-03 1.19e+00 pdb=" CG HIS E 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " 0.010 2.00e-02 2.50e+03 8.82e-03 1.17e+00 pdb=" CG HIS C 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " 0.004 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 999 2.87 - 3.38: 2267 3.38 - 3.89: 4023 3.89 - 4.39: 4241 4.39 - 4.90: 8686 Nonbonded interactions: 20216 Sorted by model distance: nonbonded pdb=" ND1 HIS A 50 " pdb=" OD1 ASP A 51 " model vdw 2.364 3.120 nonbonded pdb=" ND1 HIS E 50 " pdb=" OD1 ASP E 51 " model vdw 2.364 3.120 nonbonded pdb=" ND1 HIS C 50 " pdb=" OD1 ASP C 51 " model vdw 2.365 3.120 nonbonded pdb=" ND2 ASN A 65 " pdb=" O GLY A 68 " model vdw 2.370 3.120 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.370 3.120 ... (remaining 20211 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.000 Process input model: 3.640 Find NCS groups from input model: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 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 0.029 2649 Z= 0.323 Angle : 0.797 5.430 3588 Z= 0.466 Chirality : 0.058 0.168 477 Planarity : 0.003 0.010 444 Dihedral : 14.739 69.568 906 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % 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: -5.03 (0.30), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.23), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.004 TYR B 39 PHE 0.006 0.001 PHE E 94 HIS 0.006 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00657 ( 2649) covalent geometry : angle 0.79655 ( 3588) hydrogen bonds : bond 0.13926 ( 21) hydrogen bonds : angle 6.83160 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.101 Fit side-chains REVERT: A 57 GLU cc_start: 0.7112 (tt0) cc_final: 0.6454 (tm-30) REVERT: B 45 LYS cc_start: 0.5993 (mttt) cc_final: 0.5729 (tttt) REVERT: B 97 LYS cc_start: 0.6675 (mttm) cc_final: 0.6342 (mmtp) REVERT: C 57 GLU cc_start: 0.6460 (tt0) cc_final: 0.6020 (tm-30) REVERT: D 57 GLU cc_start: 0.6186 (tt0) cc_final: 0.5933 (tt0) REVERT: E 57 GLU cc_start: 0.6605 (tt0) cc_final: 0.6141 (tm-30) REVERT: F 97 LYS cc_start: 0.5938 (mttm) cc_final: 0.5541 (mmtp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1141 time to fit residues: 4.6530 Evaluate side-chains 29 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.149631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.119833 restraints weight = 3088.842| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.93 r_work: 0.3833 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2649 Z= 0.197 Angle : 0.606 5.026 3588 Z= 0.341 Chirality : 0.054 0.169 477 Planarity : 0.002 0.008 444 Dihedral : 5.128 15.288 375 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.72 % Allowed : 15.05 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.41 (0.32), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.24), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR A 39 PHE 0.011 0.003 PHE C 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 2649) covalent geometry : angle 0.60638 ( 3588) hydrogen bonds : bond 0.02108 ( 21) hydrogen bonds : angle 4.54348 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.6328 (tttm) cc_final: 0.5932 (mptt) REVERT: C 57 GLU cc_start: 0.6493 (tt0) cc_final: 0.5794 (tm-30) REVERT: E 57 GLU cc_start: 0.6892 (tt0) cc_final: 0.6247 (tm-30) REVERT: F 97 LYS cc_start: 0.7197 (mttm) cc_final: 0.6991 (mmtp) outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.0829 time to fit residues: 2.6055 Evaluate side-chains 27 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.150462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.121416 restraints weight = 3108.057| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.90 r_work: 0.3800 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2649 Z= 0.188 Angle : 0.565 4.527 3588 Z= 0.321 Chirality : 0.053 0.164 477 Planarity : 0.002 0.008 444 Dihedral : 4.932 15.363 375 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.51 % Allowed : 13.98 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.02 (0.35), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.011 0.003 PHE B 94 HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 2649) covalent geometry : angle 0.56542 ( 3588) hydrogen bonds : bond 0.02044 ( 21) hydrogen bonds : angle 4.16006 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.094 Fit side-chains REVERT: B 60 LYS cc_start: 0.6382 (tttm) cc_final: 0.5807 (mptt) REVERT: C 57 GLU cc_start: 0.6583 (tt0) cc_final: 0.5789 (tm-30) REVERT: D 60 LYS cc_start: 0.6450 (tttm) cc_final: 0.5720 (mptt) REVERT: E 57 GLU cc_start: 0.6888 (tt0) cc_final: 0.6077 (tm-30) REVERT: F 97 LYS cc_start: 0.7669 (mttm) cc_final: 0.7377 (mttt) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.0657 time to fit residues: 2.7611 Evaluate side-chains 33 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 overall best weight: 4.5386 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.139600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.112284 restraints weight = 3238.028| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.91 r_work: 0.3759 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2649 Z= 0.272 Angle : 0.661 5.154 3588 Z= 0.377 Chirality : 0.056 0.167 477 Planarity : 0.003 0.010 444 Dihedral : 5.432 15.605 375 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 4.30 % Allowed : 12.90 % Favored : 82.80 % 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: -4.10 (0.36), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR A 39 PHE 0.012 0.003 PHE D 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 2649) covalent geometry : angle 0.66077 ( 3588) hydrogen bonds : bond 0.01870 ( 21) hydrogen bonds : angle 4.11970 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.060 Fit side-chains REVERT: A 38 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7292 (pt) REVERT: A 57 GLU cc_start: 0.7174 (tt0) cc_final: 0.6148 (tm-30) REVERT: B 37 VAL cc_start: 0.4904 (OUTLIER) cc_final: 0.4626 (m) REVERT: C 57 GLU cc_start: 0.6747 (tt0) cc_final: 0.6039 (tm-30) REVERT: E 38 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6454 (pp) REVERT: E 57 GLU cc_start: 0.7019 (tt0) cc_final: 0.6117 (tm-30) REVERT: F 37 VAL cc_start: 0.4652 (OUTLIER) cc_final: 0.4275 (m) outliers start: 12 outliers final: 7 residues processed: 40 average time/residue: 0.0488 time to fit residues: 2.3245 Evaluate side-chains 39 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.142054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.114831 restraints weight = 3214.497| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.87 r_work: 0.3814 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2649 Z= 0.151 Angle : 0.517 3.694 3588 Z= 0.295 Chirality : 0.052 0.153 477 Planarity : 0.002 0.007 444 Dihedral : 4.697 14.644 375 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.66 % Allowed : 12.19 % Favored : 83.15 % 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: -3.91 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 39 PHE 0.008 0.002 PHE F 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2649) covalent geometry : angle 0.51663 ( 3588) hydrogen bonds : bond 0.01668 ( 21) hydrogen bonds : angle 3.95873 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.091 Fit side-chains REVERT: B 37 VAL cc_start: 0.4894 (OUTLIER) cc_final: 0.4639 (m) REVERT: B 60 LYS cc_start: 0.6507 (tttm) cc_final: 0.5918 (mmtm) REVERT: D 37 VAL cc_start: 0.5870 (OUTLIER) cc_final: 0.5520 (m) REVERT: D 60 LYS cc_start: 0.6251 (tttm) cc_final: 0.5758 (mptt) REVERT: E 38 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6515 (pp) REVERT: E 72 THR cc_start: 0.8733 (m) cc_final: 0.8495 (m) REVERT: F 37 VAL cc_start: 0.4746 (OUTLIER) cc_final: 0.4392 (m) outliers start: 13 outliers final: 7 residues processed: 36 average time/residue: 0.0948 time to fit residues: 3.9225 Evaluate side-chains 35 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.138591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.111405 restraints weight = 3158.864| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.89 r_work: 0.3753 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2649 Z= 0.217 Angle : 0.593 4.576 3588 Z= 0.338 Chirality : 0.054 0.163 477 Planarity : 0.002 0.009 444 Dihedral : 4.987 14.988 375 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.66 % Allowed : 11.47 % Favored : 83.87 % 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: -3.89 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 39 PHE 0.010 0.002 PHE F 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 2649) covalent geometry : angle 0.59339 ( 3588) hydrogen bonds : bond 0.01649 ( 21) hydrogen bonds : angle 3.94309 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.057 Fit side-chains REVERT: A 57 GLU cc_start: 0.7106 (tt0) cc_final: 0.6058 (tm-30) REVERT: D 37 VAL cc_start: 0.5803 (OUTLIER) cc_final: 0.5483 (m) REVERT: E 38 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6395 (pp) REVERT: F 37 VAL cc_start: 0.4654 (OUTLIER) cc_final: 0.4316 (m) outliers start: 13 outliers final: 7 residues processed: 38 average time/residue: 0.0531 time to fit residues: 2.3726 Evaluate side-chains 36 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.0050 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.6800 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.137543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.110301 restraints weight = 3200.868| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.93 r_work: 0.3751 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2649 Z= 0.224 Angle : 0.611 4.548 3588 Z= 0.348 Chirality : 0.054 0.164 477 Planarity : 0.002 0.009 444 Dihedral : 5.024 14.896 375 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 3.94 % Allowed : 12.54 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.95 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR A 39 PHE 0.010 0.003 PHE F 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 2649) covalent geometry : angle 0.61078 ( 3588) hydrogen bonds : bond 0.01758 ( 21) hydrogen bonds : angle 3.92644 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.066 Fit side-chains REVERT: A 57 GLU cc_start: 0.7174 (tt0) cc_final: 0.6097 (tm-30) REVERT: E 38 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6408 (pp) outliers start: 11 outliers final: 7 residues processed: 37 average time/residue: 0.0703 time to fit residues: 3.0900 Evaluate side-chains 37 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.148909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.121499 restraints weight = 3017.843| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.79 r_work: 0.3846 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2649 Z= 0.304 Angle : 0.722 5.422 3588 Z= 0.409 Chirality : 0.058 0.172 477 Planarity : 0.003 0.011 444 Dihedral : 5.413 15.492 375 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 3.23 % Allowed : 13.26 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.17 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR A 39 PHE 0.012 0.003 PHE F 94 HIS 0.009 0.005 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 2649) covalent geometry : angle 0.72214 ( 3588) hydrogen bonds : bond 0.01913 ( 21) hydrogen bonds : angle 4.04788 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.077 Fit side-chains REVERT: A 57 GLU cc_start: 0.7271 (tt0) cc_final: 0.6221 (tm-30) REVERT: C 57 GLU cc_start: 0.6829 (tt0) cc_final: 0.6159 (tm-30) REVERT: E 38 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6613 (pp) REVERT: E 57 GLU cc_start: 0.7024 (tt0) cc_final: 0.6122 (tm-30) outliers start: 9 outliers final: 8 residues processed: 39 average time/residue: 0.0818 time to fit residues: 3.6558 Evaluate side-chains 39 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.151427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.123962 restraints weight = 3036.397| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.82 r_work: 0.3872 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2649 Z= 0.211 Angle : 0.634 6.016 3588 Z= 0.357 Chirality : 0.055 0.162 477 Planarity : 0.002 0.008 444 Dihedral : 4.974 14.904 375 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.23 % Allowed : 13.98 % Favored : 82.80 % 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: -4.11 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR A 39 PHE 0.010 0.002 PHE F 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 2649) covalent geometry : angle 0.63399 ( 3588) hydrogen bonds : bond 0.01758 ( 21) hydrogen bonds : angle 3.93568 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.062 Fit side-chains REVERT: A 57 GLU cc_start: 0.7173 (tt0) cc_final: 0.6127 (tm-30) REVERT: E 38 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6523 (pp) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.0834 time to fit residues: 3.2718 Evaluate side-chains 34 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 0.0570 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.152223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.124882 restraints weight = 2990.697| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.80 r_work: 0.3886 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2649 Z= 0.189 Angle : 0.601 5.800 3588 Z= 0.338 Chirality : 0.053 0.159 477 Planarity : 0.002 0.008 444 Dihedral : 4.798 14.766 375 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.51 % Allowed : 13.98 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.03 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 39 PHE 0.009 0.002 PHE F 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 2649) covalent geometry : angle 0.60072 ( 3588) hydrogen bonds : bond 0.01639 ( 21) hydrogen bonds : angle 3.85148 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.092 Fit side-chains REVERT: A 57 GLU cc_start: 0.7134 (tt0) cc_final: 0.6128 (tm-30) REVERT: E 38 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6559 (pp) outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.0871 time to fit residues: 3.0544 Evaluate side-chains 30 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.153794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.127800 restraints weight = 3100.438| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.88 r_work: 0.3932 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2649 Z= 0.220 Angle : 0.630 5.659 3588 Z= 0.355 Chirality : 0.054 0.164 477 Planarity : 0.002 0.009 444 Dihedral : 4.942 14.964 375 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.87 % Allowed : 13.98 % Favored : 83.15 % 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: -4.04 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR A 39 PHE 0.009 0.002 PHE F 94 HIS 0.008 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 2649) covalent geometry : angle 0.62952 ( 3588) hydrogen bonds : bond 0.01728 ( 21) hydrogen bonds : angle 4.03729 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 616.71 seconds wall clock time: 11 minutes 14.45 seconds (674.45 seconds total)