Starting phenix.real_space_refine on Fri Aug 22 13:39:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adu_15370/08_2025/8adu_15370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adu_15370/08_2025/8adu_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_15370/08_2025/8adu_15370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adu_15370/08_2025/8adu_15370.map" model { file = "/net/cci-nas-00/data/ceres_data/8adu_15370/08_2025/8adu_15370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adu_15370/08_2025/8adu_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-2.0-5787/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: 0.77, per 1000 atoms: 0.22 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: 0.29 Conformation dependent library (CDL) restraints added in 159.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.15 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: 0.56 Time building geometry restraints manager: 0.40 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: 1.350 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: 0.020 Set scattering table: 0.020 Process input model: 5.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.390 ------------------------------------------------------------------------------- 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 aren 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 : 0.136 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: 0.0610 time to fit residues: 6.8501 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 : 0.136 ------------------------------------------------------------------------------- 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 aren 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 : 0.141 Fit side-chains REVERT: A 60 LYS cc_start: 0.7926 (tttm) cc_final: 0.7554 (ttmm) REVERT: B 60 LYS cc_start: 0.7870 (tttm) cc_final: 0.7480 (ttmm) REVERT: C 60 LYS cc_start: 0.7854 (tttm) cc_final: 0.7488 (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: 0.0565 time to fit residues: 6.5435 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 : 0.133 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.103384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.087113 restraints weight = 5205.460| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.51 r_work: 0.3311 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1496 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 6.876 4660 Z= 0.449 Chirality : 0.055 0.185 580 Planarity : 0.004 0.011 585 Dihedral : 5.994 20.076 495 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 7.25 % Allowed : 15.94 % 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 aren 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 0.016 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 0.00905 ( 3475) covalent geometry : angle 0.84207 ( 4660) hydrogen bonds : bond 0.03907 ( 76) hydrogen bonds : angle 5.88916 ( 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 97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.141 Fit side-chains REVERT: A 60 LYS cc_start: 0.7855 (tttm) cc_final: 0.7551 (ttmm) REVERT: B 60 LYS cc_start: 0.7892 (tttm) cc_final: 0.7505 (ttmm) REVERT: C 60 LYS cc_start: 0.7796 (tttm) cc_final: 0.7494 (ttmm) REVERT: D 60 LYS cc_start: 0.8007 (tttm) cc_final: 0.7616 (ttmm) outliers start: 25 outliers final: 18 residues processed: 90 average time/residue: 0.0682 time to fit residues: 7.6155 Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.114320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098202 restraints weight = 4898.731| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.46 r_work: 0.3507 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3475 Z= 0.140 Angle : 0.602 6.656 4660 Z= 0.320 Chirality : 0.049 0.137 580 Planarity : 0.002 0.010 585 Dihedral : 4.707 15.782 495 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % 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 aren 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 0.00299 ( 3475) covalent geometry : angle 0.60249 ( 4660) hydrogen bonds : bond 0.02522 ( 76) hydrogen bonds : angle 5.20232 ( 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 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.138 Fit side-chains REVERT: A 12 LYS cc_start: 0.7534 (mptt) cc_final: 0.6392 (tppt) REVERT: A 60 LYS cc_start: 0.7890 (tttm) cc_final: 0.7540 (ttmm) REVERT: B 60 LYS cc_start: 0.7985 (tttm) cc_final: 0.7581 (ttmm) REVERT: C 46 GLU cc_start: 0.9042 (pm20) cc_final: 0.8825 (pm20) REVERT: C 60 LYS cc_start: 0.7863 (tttm) cc_final: 0.7516 (ttmm) REVERT: D 5 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7155 (tpt) REVERT: D 46 GLU cc_start: 0.9100 (pm20) cc_final: 0.8836 (pm20) REVERT: D 60 LYS cc_start: 0.8063 (tttm) cc_final: 0.7030 (ttmm) REVERT: E 61 GLU cc_start: 0.7580 (mp0) cc_final: 0.6592 (mp0) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 0.0709 time to fit residues: 7.6690 Evaluate side-chains 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 5 MET 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: 5.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.109547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093279 restraints weight = 5000.986| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.48 r_work: 0.3418 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3475 Z= 0.224 Angle : 0.658 6.761 4660 Z= 0.348 Chirality : 0.050 0.140 580 Planarity : 0.003 0.010 585 Dihedral : 4.917 15.414 495 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 7.25 % Allowed : 18.55 % 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 aren 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 0.020 0.005 PHE C 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 3475) covalent geometry : angle 0.65774 ( 4660) hydrogen bonds : bond 0.02896 ( 76) hydrogen bonds : angle 5.20289 ( 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: 25 poor density : 78 time to evaluate : 0.123 Fit side-chains REVERT: A 10 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7619 (ptpp) REVERT: A 12 LYS cc_start: 0.7591 (mptt) cc_final: 0.6775 (tppt) REVERT: A 60 LYS cc_start: 0.7869 (tttm) cc_final: 0.7541 (ttmm) REVERT: B 60 LYS cc_start: 0.7893 (tttm) cc_final: 0.7506 (ttmm) REVERT: C 5 MET cc_start: 0.7175 (ttt) cc_final: 0.6897 (ttm) REVERT: C 10 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7338 (ptpp) REVERT: C 35 GLU cc_start: 0.8591 (tt0) cc_final: 0.8376 (tt0) REVERT: C 60 LYS cc_start: 0.7817 (tttm) cc_final: 0.7480 (ttmm) REVERT: D 60 LYS cc_start: 0.7939 (tttm) cc_final: 0.7584 (ttmm) outliers start: 25 outliers final: 19 residues processed: 93 average time/residue: 0.0743 time to fit residues: 8.3367 Evaluate side-chains 98 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS 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 C residue 10 LYS 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 10 LYS 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: 5.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.112009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.095543 restraints weight = 4967.509| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.51 r_work: 0.3454 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3475 Z= 0.180 Angle : 0.624 6.070 4660 Z= 0.331 Chirality : 0.049 0.141 580 Planarity : 0.002 0.010 585 Dihedral : 4.755 15.305 495 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.67 % Allowed : 20.58 % Favored : 72.75 % 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 aren not related in a simple way. whole: -4.32 (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 0.015 0.003 TYR E 39 PHE 0.019 0.004 PHE C 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3475) covalent geometry : angle 0.62447 ( 4660) hydrogen bonds : bond 0.02635 ( 76) hydrogen bonds : angle 5.05405 ( 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 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.163 Fit side-chains REVERT: A 12 LYS cc_start: 0.7584 (mptt) cc_final: 0.6778 (tppt) REVERT: A 60 LYS cc_start: 0.7854 (tttm) cc_final: 0.7517 (ttmm) REVERT: B 60 LYS cc_start: 0.7886 (tttm) cc_final: 0.7503 (ttmm) REVERT: C 5 MET cc_start: 0.7146 (ttt) cc_final: 0.6860 (ttm) REVERT: C 35 GLU cc_start: 0.8682 (tt0) cc_final: 0.8389 (tt0) REVERT: C 60 LYS cc_start: 0.7874 (tttm) cc_final: 0.7554 (ttmm) REVERT: D 46 GLU cc_start: 0.9130 (pm20) cc_final: 0.8880 (pm20) REVERT: D 60 LYS cc_start: 0.7949 (tttm) cc_final: 0.7363 (tttm) outliers start: 23 outliers final: 19 residues processed: 94 average time/residue: 0.0722 time to fit residues: 8.2854 Evaluate side-chains 97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 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 10 LYS 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: 0.7980 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.109930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093492 restraints weight = 5114.457| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.52 r_work: 0.3438 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3475 Z= 0.213 Angle : 0.654 6.313 4660 Z= 0.348 Chirality : 0.050 0.145 580 Planarity : 0.003 0.010 585 Dihedral : 4.820 16.136 495 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % 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 aren not related in a simple way. whole: -4.32 (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 0.015 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 0.00453 ( 3475) covalent geometry : angle 0.65433 ( 4660) hydrogen bonds : bond 0.02761 ( 76) hydrogen bonds : angle 5.09421 ( 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: 23 poor density : 81 time to evaluate : 0.095 Fit side-chains REVERT: A 8 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 12 LYS cc_start: 0.7633 (mptt) cc_final: 0.6782 (tppt) REVERT: A 60 LYS cc_start: 0.7850 (tttm) cc_final: 0.7517 (ttmm) REVERT: B 60 LYS cc_start: 0.7835 (tttm) cc_final: 0.7453 (ttmm) REVERT: C 5 MET cc_start: 0.7154 (ttt) cc_final: 0.6920 (ttm) REVERT: C 9 SER cc_start: 0.8302 (t) cc_final: 0.8100 (t) REVERT: C 60 LYS cc_start: 0.7861 (tttm) cc_final: 0.7545 (ttmm) REVERT: D 60 LYS cc_start: 0.7978 (tttm) cc_final: 0.7414 (tttm) outliers start: 23 outliers final: 20 residues processed: 95 average time/residue: 0.0641 time to fit residues: 7.5805 Evaluate side-chains 102 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 0.0770 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.110980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094518 restraints weight = 4979.924| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.52 r_work: 0.3463 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3475 Z= 0.192 Angle : 0.649 6.503 4660 Z= 0.345 Chirality : 0.050 0.145 580 Planarity : 0.003 0.010 585 Dihedral : 4.743 16.257 495 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 6.67 % Allowed : 20.29 % 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 aren not related in a simple way. whole: -4.32 (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 0.017 0.003 TYR E 39 PHE 0.019 0.004 PHE C 94 HIS 0.000 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3475) covalent geometry : angle 0.64922 ( 4660) hydrogen bonds : bond 0.02646 ( 76) hydrogen bonds : angle 5.01980 ( 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 : 0.166 Fit side-chains REVERT: A 8 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 12 LYS cc_start: 0.7654 (mptt) cc_final: 0.6834 (tppt) REVERT: A 60 LYS cc_start: 0.7873 (tttm) cc_final: 0.7541 (ttmm) REVERT: B 60 LYS cc_start: 0.7911 (tttm) cc_final: 0.7541 (ttmm) REVERT: C 60 LYS cc_start: 0.7913 (tttm) cc_final: 0.7590 (ttmm) REVERT: D 46 GLU cc_start: 0.9117 (pm20) cc_final: 0.8859 (pm20) REVERT: D 60 LYS cc_start: 0.8016 (tttm) cc_final: 0.7438 (tttm) outliers start: 23 outliers final: 22 residues processed: 94 average time/residue: 0.0636 time to fit residues: 7.4530 Evaluate side-chains 102 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU 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 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 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.0060 chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.118153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.100787 restraints weight = 4958.323| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.63 r_work: 0.3580 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3475 Z= 0.104 Angle : 0.574 6.771 4660 Z= 0.304 Chirality : 0.048 0.138 580 Planarity : 0.002 0.010 585 Dihedral : 4.119 15.062 495 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 5.22 % Allowed : 22.90 % Favored : 71.88 % 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 aren not related in a simple way. whole: -4.28 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.015 0.003 PHE C 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 3475) covalent geometry : angle 0.57363 ( 4660) hydrogen bonds : bond 0.02114 ( 76) hydrogen bonds : angle 4.68119 ( 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 104 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.138 Fit side-chains REVERT: A 12 LYS cc_start: 0.7678 (mptt) cc_final: 0.6854 (tppt) REVERT: A 35 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 60 LYS cc_start: 0.7768 (tttm) cc_final: 0.7418 (ttmm) REVERT: B 60 LYS cc_start: 0.7755 (tttm) cc_final: 0.7182 (tttm) REVERT: C 60 LYS cc_start: 0.7899 (tttm) cc_final: 0.7558 (ttmm) REVERT: D 46 GLU cc_start: 0.9090 (pm20) cc_final: 0.8843 (pm20) REVERT: D 60 LYS cc_start: 0.7940 (tttm) cc_final: 0.7111 (tttm) REVERT: E 61 GLU cc_start: 0.7659 (mp0) cc_final: 0.7049 (mp0) outliers start: 18 outliers final: 13 residues processed: 96 average time/residue: 0.0622 time to fit residues: 7.4774 Evaluate side-chains 96 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.108135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.090872 restraints weight = 5127.498| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.59 r_work: 0.3423 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3475 Z= 0.195 Angle : 0.679 7.401 4660 Z= 0.356 Chirality : 0.049 0.147 580 Planarity : 0.003 0.010 585 Dihedral : 4.552 16.472 495 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 3.77 % Allowed : 24.64 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.23 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.004 TYR E 39 PHE 0.020 0.005 PHE D 4 HIS 0.001 0.000 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 3475) covalent geometry : angle 0.67864 ( 4660) hydrogen bonds : bond 0.02602 ( 76) hydrogen bonds : angle 4.96420 ( 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 92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.132 Fit side-chains REVERT: A 12 LYS cc_start: 0.7677 (mptt) cc_final: 0.6832 (tppt) REVERT: A 60 LYS cc_start: 0.7894 (tttm) cc_final: 0.7567 (ttmm) REVERT: B 60 LYS cc_start: 0.7925 (tttm) cc_final: 0.7524 (ttmm) REVERT: C 60 LYS cc_start: 0.7916 (tttm) cc_final: 0.7593 (ttmm) REVERT: D 60 LYS cc_start: 0.8002 (tttm) cc_final: 0.7425 (tttm) outliers start: 13 outliers final: 13 residues processed: 85 average time/residue: 0.0662 time to fit residues: 6.9849 Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.115851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098460 restraints weight = 4995.837| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.61 r_work: 0.3551 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3475 Z= 0.117 Angle : 0.616 6.824 4660 Z= 0.322 Chirality : 0.048 0.140 580 Planarity : 0.002 0.009 585 Dihedral : 4.218 17.035 495 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 4.06 % Allowed : 24.64 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.18 (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 0.011 0.002 TYR E 39 PHE 0.016 0.004 PHE C 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 3475) covalent geometry : angle 0.61558 ( 4660) hydrogen bonds : bond 0.02151 ( 76) hydrogen bonds : angle 4.64811 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1048.67 seconds wall clock time: 18 minutes 48.93 seconds (1128.93 seconds total)