Starting phenix.real_space_refine on Tue Feb 3 12:54:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9je8_61410/02_2026/9je8_61410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9je8_61410/02_2026/9je8_61410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9je8_61410/02_2026/9je8_61410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9je8_61410/02_2026/9je8_61410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9je8_61410/02_2026/9je8_61410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9je8_61410/02_2026/9je8_61410.map" } resolution = 3.6 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= 0.001 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 1608 2.51 5 N 438 2.21 5 O 516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 2562 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 427 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Restraints were copied for chains: E, C, F, D, G Time building chain proxies: 0.52, per 1000 atoms: 0.20 Number of scatterers: 2562 At special positions: 0 Unit cell: (87.98, 92.13, 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 516 8.00 N 438 7.00 C 1608 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: 0.22 Conformation dependent library (CDL) restraints added in 118.3 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 50 removed outlier: 6.842A pdb=" N VAL C 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS C 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 54 through 57 removed outlier: 6.771A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 68 removed outlier: 7.040A pdb=" N ASN C 65 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 66 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY C 67 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU B 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR D 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N VAL B 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N GLY D 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 67 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.261A pdb=" N ALA B 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 46 through 50 removed outlier: 6.851A pdb=" N VAL F 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL E 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N HIS F 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLU E 46 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL G 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 57 removed outlier: 6.772A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLU G 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA E 56 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 68 removed outlier: 7.054A pdb=" N ASN F 65 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL E 66 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY F 67 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU E 61 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR G 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N VAL E 63 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL G 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ASN E 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N GLY G 68 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY E 67 " --> pdb=" O GLY G 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 76 through 78 removed outlier: 6.262A pdb=" N ALA E 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) 20 hydrogen bonds defined for protein. 60 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: 0.18 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 444 1.29 - 1.35: 390 1.35 - 1.42: 108 1.42 - 1.48: 433 1.48 - 1.54: 1199 Bond restraints: 2574 Sorted by residual: bond pdb=" CB VAL C 63 " pdb=" CG2 VAL C 63 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" CB VAL D 63 " pdb=" CG2 VAL D 63 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB VAL B 63 " pdb=" CG2 VAL B 63 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB VAL E 63 " pdb=" CG2 VAL E 63 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" CB VAL F 63 " pdb=" CG2 VAL F 63 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.86e+00 ... (remaining 2569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 2924 0.91 - 1.82: 441 1.82 - 2.74: 67 2.74 - 3.65: 36 3.65 - 4.56: 18 Bond angle restraints: 3486 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 122.59 119.23 3.36 1.57e+00 4.06e-01 4.58e+00 angle pdb=" C VAL G 49 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " ideal model delta sigma weight residual 122.59 119.24 3.35 1.57e+00 4.06e-01 4.55e+00 angle pdb=" C VAL F 49 " pdb=" N HIS F 50 " pdb=" CA HIS F 50 " ideal model delta sigma weight residual 122.59 119.25 3.34 1.57e+00 4.06e-01 4.52e+00 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 122.59 119.28 3.31 1.57e+00 4.06e-01 4.45e+00 angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 122.59 119.29 3.30 1.57e+00 4.06e-01 4.42e+00 ... (remaining 3481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 1409 17.69 - 35.37: 85 35.37 - 53.06: 6 53.06 - 70.74: 6 70.74 - 88.43: 6 Dihedral angle restraints: 1512 sinusoidal: 510 harmonic: 1002 Sorted by residual: dihedral pdb=" CA GLN D 62 " pdb=" C GLN D 62 " pdb=" N VAL D 63 " pdb=" CA VAL D 63 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN E 62 " pdb=" C GLN E 62 " pdb=" N VAL E 63 " pdb=" CA VAL E 63 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLN G 62 " pdb=" C GLN G 62 " pdb=" N VAL G 63 " pdb=" CA VAL G 63 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1509 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.029: 199 0.029 - 0.058: 121 0.058 - 0.086: 40 0.086 - 0.115: 92 0.115 - 0.143: 16 Chirality restraints: 468 Sorted by residual: chirality pdb=" CB VAL B 63 " pdb=" CA VAL B 63 " pdb=" CG1 VAL B 63 " pdb=" CG2 VAL B 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CB VAL E 63 " pdb=" CA VAL E 63 " pdb=" CG1 VAL E 63 " pdb=" CG2 VAL E 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CB VAL C 63 " pdb=" CA VAL C 63 " pdb=" CG1 VAL C 63 " pdb=" CG2 VAL C 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 465 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 63 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C VAL F 63 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL F 63 " 0.007 2.00e-02 2.50e+03 pdb=" N THR F 64 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 63 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C VAL E 63 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL E 63 " 0.007 2.00e-02 2.50e+03 pdb=" N THR E 64 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 63 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C VAL G 63 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL G 63 " 0.007 2.00e-02 2.50e+03 pdb=" N THR G 64 " 0.006 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 707 2.80 - 3.33: 2234 3.33 - 3.85: 3910 3.85 - 4.38: 4229 4.38 - 4.90: 9000 Nonbonded interactions: 20080 Sorted by model distance: nonbonded pdb=" ND1 HIS G 50 " pdb=" OD2 ASP G 51 " model vdw 2.280 3.120 nonbonded pdb=" ND1 HIS E 50 " pdb=" OD2 ASP E 51 " model vdw 2.281 3.120 nonbonded pdb=" ND1 HIS F 50 " pdb=" OD2 ASP F 51 " model vdw 2.281 3.120 nonbonded pdb=" ND1 HIS C 50 " pdb=" OD2 ASP C 51 " model vdw 2.281 3.120 nonbonded pdb=" ND1 HIS D 50 " pdb=" OD2 ASP D 51 " model vdw 2.282 3.120 ... (remaining 20075 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 'B' selection = chain 'E' selection = chain 'C' selection = chain 'F' selection = chain 'D' selection = chain 'G' } 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.540 Find NCS groups from input model: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 0.046 2574 Z= 0.350 Angle : 0.775 4.562 3486 Z= 0.436 Chirality : 0.060 0.143 468 Planarity : 0.003 0.011 426 Dihedral : 14.232 88.428 876 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.61 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR E 39 PHE 0.013 0.004 PHE G 94 HIS 0.006 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00750 ( 2574) covalent geometry : angle 0.77469 ( 3486) hydrogen bonds : bond 0.18321 ( 20) hydrogen bonds : angle 7.41732 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.098 Fit side-chains REVERT: B 83 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8197 (mp0) REVERT: C 83 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8091 (mp0) REVERT: F 83 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7865 (mp0) REVERT: D 58 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8559 (mmmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0768 time to fit residues: 3.6336 Evaluate side-chains 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 65 ASN E 62 GLN E 65 ASN C 62 GLN C 65 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 65 ASN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 65 ASN G 62 GLN G 65 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.138515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.119745 restraints weight = 3017.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.123519 restraints weight = 1447.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.125900 restraints weight = 866.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.127610 restraints weight = 600.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.128734 restraints weight = 457.675| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2574 Z= 0.125 Angle : 0.549 4.946 3486 Z= 0.301 Chirality : 0.054 0.130 468 Planarity : 0.002 0.011 426 Dihedral : 5.082 18.255 366 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.48 % Allowed : 9.63 % Favored : 88.89 % 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: -4.86 (0.37), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR E 39 PHE 0.011 0.002 PHE B 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2574) covalent geometry : angle 0.54854 ( 3486) hydrogen bonds : bond 0.01926 ( 20) hydrogen bonds : angle 4.83417 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.058 Fit side-chains REVERT: B 83 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8131 (mp0) REVERT: E 58 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8480 (mmmm) REVERT: D 58 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8649 (mmmm) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.0483 time to fit residues: 2.1867 Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 0.0040 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.0000 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.136224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117158 restraints weight = 3004.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.121168 restraints weight = 1365.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123771 restraints weight = 795.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.125527 restraints weight = 536.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.126745 restraints weight = 400.154| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2574 Z= 0.107 Angle : 0.513 4.920 3486 Z= 0.280 Chirality : 0.052 0.128 468 Planarity : 0.002 0.011 426 Dihedral : 4.788 15.187 366 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.96 % Allowed : 8.89 % Favored : 88.15 % 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: -4.28 (0.39), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR E 39 PHE 0.007 0.002 PHE E 94 HIS 0.003 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 2574) covalent geometry : angle 0.51282 ( 3486) hydrogen bonds : bond 0.01656 ( 20) hydrogen bonds : angle 4.37666 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.056 Fit side-chains REVERT: B 83 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8102 (mp0) REVERT: C 83 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7804 (mp0) REVERT: F 83 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7550 (mp0) REVERT: D 58 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8488 (mmmm) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.0564 time to fit residues: 2.8004 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain G residue 82 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.0070 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.132412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.113644 restraints weight = 3005.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.117519 restraints weight = 1435.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.119974 restraints weight = 856.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.121738 restraints weight = 592.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.122980 restraints weight = 448.883| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2574 Z= 0.193 Angle : 0.583 5.109 3486 Z= 0.319 Chirality : 0.053 0.124 468 Planarity : 0.002 0.012 426 Dihedral : 5.107 16.334 366 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 5.19 % Allowed : 9.63 % Favored : 85.19 % 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: -4.25 (0.39), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR E 39 PHE 0.010 0.002 PHE B 94 HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 2574) covalent geometry : angle 0.58264 ( 3486) hydrogen bonds : bond 0.01559 ( 20) hydrogen bonds : angle 4.41465 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.094 Fit side-chains REVERT: B 58 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8267 (mmmm) REVERT: B 83 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8132 (mp0) REVERT: C 83 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7846 (mp0) REVERT: F 83 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7761 (mp0) REVERT: D 58 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8556 (mmmm) outliers start: 14 outliers final: 10 residues processed: 47 average time/residue: 0.0732 time to fit residues: 3.9606 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.133274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.114625 restraints weight = 3030.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.118540 restraints weight = 1412.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.121035 restraints weight = 838.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.122782 restraints weight = 575.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.124063 restraints weight = 432.640| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2574 Z= 0.162 Angle : 0.553 5.111 3486 Z= 0.304 Chirality : 0.052 0.123 468 Planarity : 0.002 0.012 426 Dihedral : 5.010 16.386 366 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.81 % Allowed : 10.37 % Favored : 84.81 % 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: -4.19 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR E 39 PHE 0.010 0.002 PHE B 94 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2574) covalent geometry : angle 0.55316 ( 3486) hydrogen bonds : bond 0.01494 ( 20) hydrogen bonds : angle 4.25604 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.095 Fit side-chains REVERT: B 58 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8272 (mmmm) REVERT: B 83 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8130 (mp0) REVERT: C 83 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7827 (mp0) REVERT: F 83 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7794 (mp0) outliers start: 13 outliers final: 11 residues processed: 49 average time/residue: 0.0862 time to fit residues: 4.8530 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain G residue 82 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 0.0980 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.0020 chunk 18 optimal weight: 6.9990 overall best weight: 0.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.148680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.131347 restraints weight = 2867.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.135036 restraints weight = 1312.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.137421 restraints weight = 759.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.139106 restraints weight = 514.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.140253 restraints weight = 383.807| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 2574 Z= 0.064 Angle : 0.417 3.917 3486 Z= 0.234 Chirality : 0.050 0.124 468 Planarity : 0.001 0.010 426 Dihedral : 4.219 13.193 366 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.96 % Allowed : 11.85 % Favored : 85.19 % 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: -3.72 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR E 39 PHE 0.005 0.001 PHE E 94 HIS 0.001 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00128 ( 2574) covalent geometry : angle 0.41737 ( 3486) hydrogen bonds : bond 0.01418 ( 20) hydrogen bonds : angle 4.01398 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.058 Fit side-chains REVERT: F 58 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8431 (mmmm) REVERT: F 83 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7703 (mp0) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 0.0717 time to fit residues: 2.7825 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 82 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.1082 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.125694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105712 restraints weight = 3226.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.109136 restraints weight = 1705.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.111596 restraints weight = 1100.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.113208 restraints weight = 798.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.114451 restraints weight = 627.375| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2574 Z= 0.172 Angle : 0.546 7.538 3486 Z= 0.296 Chirality : 0.052 0.129 468 Planarity : 0.002 0.012 426 Dihedral : 4.818 15.339 366 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.22 % Allowed : 13.33 % Favored : 84.44 % 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: -3.79 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR E 39 PHE 0.008 0.002 PHE E 94 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2574) covalent geometry : angle 0.54634 ( 3486) hydrogen bonds : bond 0.01364 ( 20) hydrogen bonds : angle 4.05142 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.093 Fit side-chains REVERT: B 83 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8092 (mp0) REVERT: C 83 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7936 (mp0) REVERT: F 83 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7758 (mp0) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.1003 time to fit residues: 4.5540 Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.140910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.122805 restraints weight = 2985.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.126557 restraints weight = 1378.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.128980 restraints weight = 817.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.130735 restraints weight = 558.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.131892 restraints weight = 421.336| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2574 Z= 0.094 Angle : 0.466 6.221 3486 Z= 0.254 Chirality : 0.050 0.127 468 Planarity : 0.002 0.011 426 Dihedral : 4.403 13.804 366 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.59 % Allowed : 13.70 % Favored : 83.70 % 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: -3.58 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 39 PHE 0.007 0.001 PHE E 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 2574) covalent geometry : angle 0.46556 ( 3486) hydrogen bonds : bond 0.01254 ( 20) hydrogen bonds : angle 3.88905 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.100 Fit side-chains REVERT: B 83 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8127 (mp0) REVERT: C 83 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7925 (mp0) REVERT: F 58 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8523 (mmmm) REVERT: F 83 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7734 (mp0) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.0926 time to fit residues: 4.1918 Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain G residue 82 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 34 optimal weight: 0.0070 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.6604 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.136295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.117697 restraints weight = 3036.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.121683 restraints weight = 1408.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.124265 restraints weight = 830.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.125992 restraints weight = 566.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.127274 restraints weight = 424.573| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2574 Z= 0.140 Angle : 0.514 6.611 3486 Z= 0.279 Chirality : 0.051 0.128 468 Planarity : 0.002 0.011 426 Dihedral : 4.673 14.751 366 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 1.48 % Allowed : 15.19 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.58 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR E 39 PHE 0.007 0.002 PHE E 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2574) covalent geometry : angle 0.51373 ( 3486) hydrogen bonds : bond 0.01354 ( 20) hydrogen bonds : angle 3.93943 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.100 Fit side-chains REVERT: B 83 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8154 (mp0) REVERT: C 83 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7881 (mp0) REVERT: F 83 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7744 (mp0) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.0996 time to fit residues: 4.7664 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain G residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 16 optimal weight: 0.0000 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.130607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.112034 restraints weight = 3101.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.115963 restraints weight = 1452.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.118468 restraints weight = 864.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.120238 restraints weight = 595.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121497 restraints weight = 446.630| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2574 Z= 0.223 Angle : 0.600 7.163 3486 Z= 0.327 Chirality : 0.053 0.125 468 Planarity : 0.002 0.013 426 Dihedral : 5.094 16.544 366 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 2.59 % Allowed : 13.70 % Favored : 83.70 % 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: -3.77 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.004 TYR E 39 PHE 0.009 0.002 PHE E 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 2574) covalent geometry : angle 0.60017 ( 3486) hydrogen bonds : bond 0.01461 ( 20) hydrogen bonds : angle 4.09881 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.100 Fit side-chains REVERT: B 83 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8159 (mp0) REVERT: C 83 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7894 (mp0) REVERT: F 83 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7779 (mp0) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.0967 time to fit residues: 4.5389 Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain G residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 0.0060 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.141797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.123937 restraints weight = 2975.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.127699 restraints weight = 1359.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.130156 restraints weight = 795.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.131873 restraints weight = 539.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.133079 restraints weight = 404.796| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2574 Z= 0.084 Angle : 0.455 5.820 3486 Z= 0.249 Chirality : 0.050 0.126 468 Planarity : 0.002 0.010 426 Dihedral : 4.401 14.098 366 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.48 % Allowed : 15.56 % Favored : 82.96 % 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: -3.48 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 39 PHE 0.006 0.001 PHE E 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00179 ( 2574) covalent geometry : angle 0.45471 ( 3486) hydrogen bonds : bond 0.01344 ( 20) hydrogen bonds : angle 3.93919 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 667.39 seconds wall clock time: 12 minutes 16.95 seconds (736.95 seconds total)