Starting phenix.real_space_refine on Tue Feb 3 13:50:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adu_15370/02_2026/8adu_15370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adu_15370/02_2026/8adu_15370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8adu_15370/02_2026/8adu_15370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adu_15370/02_2026/8adu_15370.map" model { file = "/net/cci-nas-00/data/ceres_data/8adu_15370/02_2026/8adu_15370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adu_15370/02_2026/8adu_15370.cif" } resolution = 3.24 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2160 2.51 5 N 600 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3460 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.50, per 1000 atoms: 0.14 Number of scatterers: 3460 At special positions: 0 Unit cell: (86.1, 97.65, 39.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 690 8.00 N 600 7.00 C 2160 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: 0.19 Conformation dependent library (CDL) restraints added in 89.7 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.880A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU E 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA D 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.207A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN C 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN D 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 78 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 94 76 hydrogen bonds defined for protein. 228 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: 0.42 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1145 1.34 - 1.45: 439 1.45 - 1.57: 1871 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 3475 Sorted by residual: bond pdb=" CB VAL E 15 " pdb=" CG2 VAL E 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB VAL A 15 " pdb=" CG2 VAL A 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.69e+00 bond pdb=" CB VAL D 15 " pdb=" CG2 VAL D 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL C 15 " pdb=" CG2 VAL C 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL B 15 " pdb=" CG2 VAL B 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 ... (remaining 3470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 3777 0.88 - 1.77: 660 1.77 - 2.65: 153 2.65 - 3.53: 45 3.53 - 4.42: 25 Bond angle restraints: 4660 Sorted by residual: angle pdb=" CA GLN D 79 " pdb=" CB GLN D 79 " pdb=" CG GLN D 79 " ideal model delta sigma weight residual 114.10 118.52 -4.42 2.00e+00 2.50e-01 4.87e+00 angle pdb=" CA GLN A 79 " pdb=" CB GLN A 79 " pdb=" CG GLN A 79 " ideal model delta sigma weight residual 114.10 118.51 -4.41 2.00e+00 2.50e-01 4.86e+00 angle pdb=" C GLN E 79 " pdb=" CA GLN E 79 " pdb=" CB GLN E 79 " ideal model delta sigma weight residual 110.42 114.81 -4.39 1.99e+00 2.53e-01 4.86e+00 angle pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " pdb=" CG GLN C 79 " ideal model delta sigma weight residual 114.10 118.50 -4.40 2.00e+00 2.50e-01 4.85e+00 angle pdb=" C GLN C 79 " pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " ideal model delta sigma weight residual 110.42 114.80 -4.38 1.99e+00 2.53e-01 4.85e+00 ... (remaining 4655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 1904 17.35 - 34.69: 136 34.69 - 52.03: 30 52.03 - 69.38: 5 69.38 - 86.72: 15 Dihedral angle restraints: 2090 sinusoidal: 745 harmonic: 1345 Sorted by residual: dihedral pdb=" CA MET E 5 " pdb=" C MET E 5 " pdb=" N LYS E 6 " pdb=" CA LYS E 6 " ideal model delta harmonic sigma weight residual 180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET D 5 " pdb=" C MET D 5 " pdb=" N LYS D 6 " pdb=" CA LYS D 6 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET C 5 " pdb=" C MET C 5 " pdb=" N LYS C 6 " pdb=" CA LYS C 6 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 2087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 505 0.087 - 0.173: 65 0.173 - 0.260: 5 0.260 - 0.347: 0 0.347 - 0.433: 5 Chirality restraints: 580 Sorted by residual: chirality pdb=" CB VAL D 15 " pdb=" CA VAL D 15 " pdb=" CG1 VAL D 15 " pdb=" CG2 VAL D 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CB VAL E 15 " pdb=" CA VAL E 15 " pdb=" CG1 VAL E 15 " pdb=" CG2 VAL E 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CB VAL B 15 " pdb=" CA VAL B 15 " pdb=" CG1 VAL B 15 " pdb=" CG2 VAL B 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 577 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 4 " -0.010 2.00e-02 2.50e+03 9.37e-03 1.54e+00 pdb=" CG PHE E 4 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE E 4 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE E 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 4 " -0.010 2.00e-02 2.50e+03 9.22e-03 1.49e+00 pdb=" CG PHE D 4 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 4 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 4 " -0.010 2.00e-02 2.50e+03 9.20e-03 1.48e+00 pdb=" CG PHE C 4 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 4 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 4 " -0.003 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1071 2.82 - 3.34: 3134 3.34 - 3.86: 5731 3.86 - 4.38: 6806 4.38 - 4.90: 13256 Nonbonded interactions: 29998 Sorted by model distance: nonbonded pdb=" OG SER E 9 " pdb=" N LYS E 10 " model vdw 2.296 3.120 nonbonded pdb=" OG SER C 9 " pdb=" N LYS C 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER D 9 " pdb=" N LYS D 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER A 9 " pdb=" N LYS A 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER B 9 " pdb=" N LYS B 10 " model vdw 2.297 3.120 ... (remaining 29993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.210 Find NCS groups from input model: 0.030 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:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 0.057 3475 Z= 0.312 Angle : 0.820 4.415 4660 Z= 0.461 Chirality : 0.068 0.433 580 Planarity : 0.003 0.009 585 Dihedral : 15.523 86.720 1240 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.91 (0.25), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.19), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR D 39 PHE 0.022 0.005 PHE E 4 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 3475) covalent geometry : angle 0.82042 ( 4660) hydrogen bonds : bond 0.14117 ( 76) hydrogen bonds : angle 8.76871 ( 228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7926 (tttm) cc_final: 0.7707 (ttmm) REVERT: B 99 GLN cc_start: 0.4969 (tm-30) cc_final: 0.4710 (tm-30) REVERT: C 12 LYS cc_start: 0.7500 (mptt) cc_final: 0.7263 (mptt) REVERT: C 60 LYS cc_start: 0.7879 (tttm) cc_final: 0.7641 (ttmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0626 time to fit residues: 6.9768 Evaluate side-chains 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3802 r_free = 0.3802 target = 0.116386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100097 restraints weight = 4901.371| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.49 r_work: 0.3504 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3475 Z= 0.140 Angle : 0.616 7.180 4660 Z= 0.326 Chirality : 0.050 0.149 580 Planarity : 0.003 0.010 585 Dihedral : 4.569 13.671 495 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 4.35 % Allowed : 14.20 % Favored : 81.45 % 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: -4.44 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 39 PHE 0.017 0.004 PHE D 4 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3475) covalent geometry : angle 0.61559 ( 4660) hydrogen bonds : bond 0.03019 ( 76) hydrogen bonds : angle 5.81318 ( 228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.077 Fit side-chains REVERT: A 60 LYS cc_start: 0.7926 (tttm) cc_final: 0.7554 (ttmm) REVERT: A 99 GLN cc_start: 0.4555 (tm-30) cc_final: 0.4355 (tm-30) REVERT: B 60 LYS cc_start: 0.7870 (tttm) cc_final: 0.7480 (ttmm) REVERT: C 60 LYS cc_start: 0.7853 (tttm) cc_final: 0.7487 (ttmm) REVERT: D 60 LYS cc_start: 0.7900 (tttm) cc_final: 0.7429 (ttmm) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.0569 time to fit residues: 6.5291 Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 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 = 0.3638 r_free = 0.3638 target = 0.103077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086855 restraints weight = 5216.880| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.51 r_work: 0.3306 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 3475 Z= 0.420 Angle : 0.842 6.862 4660 Z= 0.449 Chirality : 0.055 0.184 580 Planarity : 0.004 0.011 585 Dihedral : 5.984 19.993 495 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 7.54 % Allowed : 15.65 % Favored : 76.81 % 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: -4.47 (0.28), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR E 39 PHE 0.026 0.006 PHE B 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00903 ( 3475) covalent geometry : angle 0.84171 ( 4660) hydrogen bonds : bond 0.03909 ( 76) hydrogen bonds : angle 5.88222 ( 228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.152 Fit side-chains REVERT: A 60 LYS cc_start: 0.7853 (tttm) cc_final: 0.7551 (ttmm) REVERT: B 60 LYS cc_start: 0.7888 (tttm) cc_final: 0.7501 (ttmm) REVERT: C 60 LYS cc_start: 0.7796 (tttm) cc_final: 0.7486 (ttmm) REVERT: D 60 LYS cc_start: 0.8000 (tttm) cc_final: 0.7610 (ttmm) outliers start: 26 outliers final: 18 residues processed: 91 average time/residue: 0.0544 time to fit residues: 6.1834 Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** ** D 24 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 = 0.3812 r_free = 0.3812 target = 0.114502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098325 restraints weight = 4887.807| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.48 r_work: 0.3512 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3475 Z= 0.138 Angle : 0.601 6.539 4660 Z= 0.319 Chirality : 0.049 0.137 580 Planarity : 0.002 0.009 585 Dihedral : 4.700 15.712 495 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 4.93 % Allowed : 18.84 % Favored : 76.23 % 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: -4.34 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.004 TYR E 39 PHE 0.016 0.004 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3475) covalent geometry : angle 0.60090 ( 4660) hydrogen bonds : bond 0.02524 ( 76) hydrogen bonds : angle 5.19162 ( 228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.132 Fit side-chains REVERT: A 12 LYS cc_start: 0.7536 (mptt) cc_final: 0.6390 (tppt) REVERT: A 60 LYS cc_start: 0.7873 (tttm) cc_final: 0.7523 (ttmm) REVERT: B 60 LYS cc_start: 0.7972 (tttm) cc_final: 0.7568 (ttmm) REVERT: C 46 GLU cc_start: 0.9042 (pm20) cc_final: 0.8826 (pm20) REVERT: C 60 LYS cc_start: 0.7851 (tttm) cc_final: 0.7502 (ttmm) REVERT: D 46 GLU cc_start: 0.9104 (pm20) cc_final: 0.8841 (pm20) REVERT: D 60 LYS cc_start: 0.8047 (tttm) cc_final: 0.7010 (ttmm) REVERT: E 61 GLU cc_start: 0.7582 (mp0) cc_final: 0.6593 (mp0) outliers start: 17 outliers final: 13 residues processed: 89 average time/residue: 0.0601 time to fit residues: 6.6753 Evaluate side-chains 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** D 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.114148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097954 restraints weight = 4969.246| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.48 r_work: 0.3510 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3475 Z= 0.147 Angle : 0.593 6.522 4660 Z= 0.313 Chirality : 0.049 0.137 580 Planarity : 0.002 0.010 585 Dihedral : 4.448 13.923 495 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 6.09 % Allowed : 19.71 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.33 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR E 39 PHE 0.018 0.004 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3475) covalent geometry : angle 0.59262 ( 4660) hydrogen bonds : bond 0.02517 ( 76) hydrogen bonds : angle 4.94716 ( 228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.129 Fit side-chains REVERT: A 12 LYS cc_start: 0.7575 (mptt) cc_final: 0.6790 (tppt) REVERT: A 60 LYS cc_start: 0.7897 (tttm) cc_final: 0.7569 (ttmm) REVERT: B 60 LYS cc_start: 0.7975 (tttm) cc_final: 0.7583 (ttmm) REVERT: C 60 LYS cc_start: 0.7864 (tttm) cc_final: 0.7546 (ttmm) REVERT: D 60 LYS cc_start: 0.7993 (tttm) cc_final: 0.6821 (tttm) REVERT: E 61 GLU cc_start: 0.7644 (mp0) cc_final: 0.6564 (mp0) outliers start: 21 outliers final: 16 residues processed: 93 average time/residue: 0.0627 time to fit residues: 7.1304 Evaluate side-chains 96 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.109450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093079 restraints weight = 5002.479| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.49 r_work: 0.3426 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3475 Z= 0.217 Angle : 0.662 6.843 4660 Z= 0.350 Chirality : 0.050 0.140 580 Planarity : 0.003 0.010 585 Dihedral : 4.773 16.400 495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.96 % Allowed : 18.84 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.31 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR E 39 PHE 0.020 0.005 PHE C 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 3475) covalent geometry : angle 0.66151 ( 4660) hydrogen bonds : bond 0.02795 ( 76) hydrogen bonds : angle 5.09638 ( 228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.125 Fit side-chains REVERT: A 8 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8386 (tt) REVERT: A 12 LYS cc_start: 0.7634 (mptt) cc_final: 0.6840 (tppt) REVERT: A 60 LYS cc_start: 0.7891 (tttm) cc_final: 0.7565 (ttmm) REVERT: B 60 LYS cc_start: 0.7877 (tttm) cc_final: 0.7481 (ttmm) REVERT: C 5 MET cc_start: 0.7167 (ttt) cc_final: 0.6892 (ttm) REVERT: C 60 LYS cc_start: 0.7856 (tttm) cc_final: 0.7526 (ttmm) REVERT: D 60 LYS cc_start: 0.7980 (tttm) cc_final: 0.7435 (tttm) REVERT: E 5 MET cc_start: 0.7388 (ttt) cc_final: 0.7127 (ttm) outliers start: 24 outliers final: 19 residues processed: 93 average time/residue: 0.0584 time to fit residues: 6.7339 Evaluate side-chains 99 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.118392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.101847 restraints weight = 5025.829| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.53 r_work: 0.3590 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3475 Z= 0.107 Angle : 0.568 6.508 4660 Z= 0.299 Chirality : 0.048 0.136 580 Planarity : 0.002 0.010 585 Dihedral : 4.117 14.659 495 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 5.22 % Allowed : 20.29 % Favored : 74.49 % 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 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR E 39 PHE 0.016 0.004 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3475) covalent geometry : angle 0.56772 ( 4660) hydrogen bonds : bond 0.02169 ( 76) hydrogen bonds : angle 4.68504 ( 228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.077 Fit side-chains REVERT: A 12 LYS cc_start: 0.7713 (mptt) cc_final: 0.6902 (tppt) REVERT: A 60 LYS cc_start: 0.7804 (tttm) cc_final: 0.7459 (ttmm) REVERT: B 5 MET cc_start: 0.6868 (tpp) cc_final: 0.6622 (tpt) REVERT: B 60 LYS cc_start: 0.7866 (tttm) cc_final: 0.7330 (tttm) REVERT: C 35 GLU cc_start: 0.8579 (tt0) cc_final: 0.8345 (tt0) REVERT: C 60 LYS cc_start: 0.7885 (tttm) cc_final: 0.7597 (ttmm) REVERT: D 46 GLU cc_start: 0.9093 (pm20) cc_final: 0.8855 (pm20) REVERT: D 60 LYS cc_start: 0.7981 (tttm) cc_final: 0.6810 (tttm) REVERT: E 61 GLU cc_start: 0.7577 (mp0) cc_final: 0.6744 (mp0) outliers start: 18 outliers final: 13 residues processed: 96 average time/residue: 0.0358 time to fit residues: 4.3709 Evaluate side-chains 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.106944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.090479 restraints weight = 5118.330| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.42 r_work: 0.3379 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3475 Z= 0.303 Angle : 0.776 7.340 4660 Z= 0.405 Chirality : 0.051 0.145 580 Planarity : 0.003 0.013 585 Dihedral : 5.089 18.305 495 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.67 % Allowed : 20.00 % Favored : 73.33 % 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: -4.30 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.006 TYR A 39 PHE 0.023 0.005 PHE B 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 3475) covalent geometry : angle 0.77641 ( 4660) hydrogen bonds : bond 0.02960 ( 76) hydrogen bonds : angle 5.20978 ( 228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.076 Fit side-chains REVERT: A 60 LYS cc_start: 0.7857 (tttm) cc_final: 0.7534 (ttmm) REVERT: B 60 LYS cc_start: 0.7927 (tttm) cc_final: 0.7509 (ttmm) REVERT: C 60 LYS cc_start: 0.7891 (tttm) cc_final: 0.7605 (ttmm) REVERT: D 12 LYS cc_start: 0.7261 (mptt) cc_final: 0.7042 (mptt) REVERT: D 60 LYS cc_start: 0.8005 (tttm) cc_final: 0.7443 (tttm) outliers start: 23 outliers final: 18 residues processed: 92 average time/residue: 0.0627 time to fit residues: 7.0845 Evaluate side-chains 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.112632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.095577 restraints weight = 5235.624| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.57 r_work: 0.3511 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3475 Z= 0.117 Angle : 0.623 6.692 4660 Z= 0.322 Chirality : 0.048 0.135 580 Planarity : 0.002 0.009 585 Dihedral : 4.251 16.235 495 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 4.06 % Allowed : 22.90 % Favored : 73.04 % 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: -4.23 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 39 PHE 0.016 0.004 PHE C 94 HIS 0.000 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3475) covalent geometry : angle 0.62322 ( 4660) hydrogen bonds : bond 0.02208 ( 76) hydrogen bonds : angle 4.72401 ( 228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.132 Fit side-chains REVERT: A 12 LYS cc_start: 0.7715 (mptt) cc_final: 0.6894 (tppt) REVERT: A 35 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: A 60 LYS cc_start: 0.7800 (tttm) cc_final: 0.7455 (ttmm) REVERT: B 60 LYS cc_start: 0.7790 (tttm) cc_final: 0.7218 (tttm) REVERT: C 60 LYS cc_start: 0.7921 (tttm) cc_final: 0.7600 (ttmm) REVERT: D 60 LYS cc_start: 0.8023 (tttm) cc_final: 0.7244 (tttm) REVERT: E 61 GLU cc_start: 0.7691 (mp0) cc_final: 0.7206 (mp0) outliers start: 14 outliers final: 13 residues processed: 90 average time/residue: 0.0445 time to fit residues: 5.1158 Evaluate side-chains 98 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084662 restraints weight = 5523.155| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.58 r_work: 0.3319 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3475 Z= 0.269 Angle : 0.754 7.058 4660 Z= 0.393 Chirality : 0.050 0.146 580 Planarity : 0.003 0.010 585 Dihedral : 4.922 18.997 495 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 4.93 % Allowed : 22.61 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.22 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.004 TYR A 39 PHE 0.021 0.005 PHE B 94 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 3475) covalent geometry : angle 0.75376 ( 4660) hydrogen bonds : bond 0.02819 ( 76) hydrogen bonds : angle 5.15610 ( 228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.079 Fit side-chains REVERT: A 12 LYS cc_start: 0.7664 (mptt) cc_final: 0.6858 (tppt) REVERT: A 60 LYS cc_start: 0.7845 (tttm) cc_final: 0.7541 (ttmm) REVERT: B 60 LYS cc_start: 0.7849 (tttm) cc_final: 0.7463 (ttmm) REVERT: C 60 LYS cc_start: 0.7892 (tttm) cc_final: 0.7609 (ttmm) REVERT: D 60 LYS cc_start: 0.8052 (tttm) cc_final: 0.7501 (tttm) outliers start: 17 outliers final: 16 residues processed: 87 average time/residue: 0.0388 time to fit residues: 4.2266 Evaluate side-chains 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.109071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.091992 restraints weight = 5340.746| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.58 r_work: 0.3452 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3475 Z= 0.143 Angle : 0.651 6.908 4660 Z= 0.338 Chirality : 0.049 0.142 580 Planarity : 0.002 0.010 585 Dihedral : 4.425 17.707 495 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 4.93 % Allowed : 22.90 % Favored : 72.17 % 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 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR E 39 PHE 0.018 0.004 PHE C 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3475) covalent geometry : angle 0.65096 ( 4660) hydrogen bonds : bond 0.02281 ( 76) hydrogen bonds : angle 4.81770 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 880.07 seconds wall clock time: 15 minutes 53.80 seconds (953.80 seconds total)