Starting phenix.real_space_refine on Tue Feb 3 12:20:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xbn_66706/02_2026/9xbn_66706.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xbn_66706/02_2026/9xbn_66706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xbn_66706/02_2026/9xbn_66706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xbn_66706/02_2026/9xbn_66706.map" model { file = "/net/cci-nas-00/data/ceres_data/9xbn_66706/02_2026/9xbn_66706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xbn_66706/02_2026/9xbn_66706.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 960 2.51 5 N 320 2.21 5 O 355 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: 1635 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 327 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.25, per 1000 atoms: 0.15 Number of scatterers: 1635 At special positions: 0 Unit cell: (62.524, 66.836, 42.042, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 355 8.00 N 320 7.00 C 960 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: 0.11 Conformation dependent library (CDL) restraints added in 65.8 milliseconds 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 340 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 8 through 16 removed outlier: 6.439A pdb=" N ASN A 8 " --> pdb=" O ASN C 9 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLN C 11 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLN A 10 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N TYR C 13 " --> pdb=" O GLN A 10 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASN A 12 " --> pdb=" O TYR C 13 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLN C 15 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A 14 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN C 8 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLN E 11 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLN C 10 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR E 13 " --> pdb=" O GLN C 10 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN C 12 " --> pdb=" O TYR E 13 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLN E 15 " --> pdb=" O ASN C 12 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN C 14 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 22 through 23 removed outlier: 6.506A pdb=" N GLN B 22 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN A 22 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.740A pdb=" N ARG B 28 " --> pdb=" O TYR D 29 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG A 28 " --> pdb=" O TYR B 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.178A pdb=" N TYR A 32 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR C 32 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.180A pdb=" N TYR B 49 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TYR D 52 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY B 51 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A 49 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TYR B 52 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY A 51 " --> pdb=" O TYR B 52 " (cutoff:3.500A) 32 hydrogen bonds defined for protein. 96 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: 0.21 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 305 1.28 - 1.35: 310 1.35 - 1.41: 245 1.41 - 1.47: 200 1.47 - 1.54: 600 Bond restraints: 1660 Sorted by residual: bond pdb=" N ASN C 48 " pdb=" CA ASN C 48 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.22e-02 6.72e+03 8.10e+00 bond pdb=" N ASN A 48 " pdb=" CA ASN A 48 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.22e-02 6.72e+03 8.00e+00 bond pdb=" N ASN B 48 " pdb=" CA ASN B 48 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.22e-02 6.72e+03 7.89e+00 bond pdb=" N ASN D 48 " pdb=" CA ASN D 48 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.22e-02 6.72e+03 7.79e+00 bond pdb=" N ASN E 48 " pdb=" CA ASN E 48 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.22e-02 6.72e+03 7.76e+00 ... (remaining 1655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 2024 1.28 - 2.57: 160 2.57 - 3.85: 26 3.85 - 5.13: 5 5.13 - 6.42: 10 Bond angle restraints: 2225 Sorted by residual: angle pdb=" N TYR D 32 " pdb=" CA TYR D 32 " pdb=" CB TYR D 32 " ideal model delta sigma weight residual 110.80 104.38 6.42 1.73e+00 3.34e-01 1.38e+01 angle pdb=" N TYR C 32 " pdb=" CA TYR C 32 " pdb=" CB TYR C 32 " ideal model delta sigma weight residual 110.80 104.39 6.41 1.73e+00 3.34e-01 1.37e+01 angle pdb=" N TYR A 32 " pdb=" CA TYR A 32 " pdb=" CB TYR A 32 " ideal model delta sigma weight residual 110.80 104.39 6.41 1.73e+00 3.34e-01 1.37e+01 angle pdb=" N TYR E 32 " pdb=" CA TYR E 32 " pdb=" CB TYR E 32 " ideal model delta sigma weight residual 110.80 104.40 6.40 1.73e+00 3.34e-01 1.37e+01 angle pdb=" N TYR B 32 " pdb=" CA TYR B 32 " pdb=" CB TYR B 32 " ideal model delta sigma weight residual 110.80 104.40 6.40 1.73e+00 3.34e-01 1.37e+01 ... (remaining 2220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 800 17.84 - 35.67: 125 35.67 - 53.51: 5 53.51 - 71.35: 15 71.35 - 89.18: 10 Dihedral angle restraints: 955 sinusoidal: 395 harmonic: 560 Sorted by residual: dihedral pdb=" N TYR C 32 " pdb=" C TYR C 32 " pdb=" CA TYR C 32 " pdb=" CB TYR C 32 " ideal model delta harmonic sigma weight residual 122.80 116.48 6.32 0 2.50e+00 1.60e-01 6.40e+00 dihedral pdb=" N TYR D 32 " pdb=" C TYR D 32 " pdb=" CA TYR D 32 " pdb=" CB TYR D 32 " ideal model delta harmonic sigma weight residual 122.80 116.48 6.32 0 2.50e+00 1.60e-01 6.38e+00 dihedral pdb=" N TYR A 32 " pdb=" C TYR A 32 " pdb=" CA TYR A 32 " pdb=" CB TYR A 32 " ideal model delta harmonic sigma weight residual 122.80 116.48 6.32 0 2.50e+00 1.60e-01 6.38e+00 ... (remaining 952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 106 0.033 - 0.065: 44 0.065 - 0.098: 10 0.098 - 0.131: 5 0.131 - 0.163: 5 Chirality restraints: 170 Sorted by residual: chirality pdb=" CA TYR B 32 " pdb=" N TYR B 32 " pdb=" C TYR B 32 " pdb=" CB TYR B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA TYR D 32 " pdb=" N TYR D 32 " pdb=" C TYR D 32 " pdb=" CB TYR D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA TYR A 32 " pdb=" N TYR A 32 " pdb=" C TYR A 32 " pdb=" CB TYR A 32 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 167 not shown) Planarity restraints: 335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 13 " -0.005 2.00e-02 2.50e+03 2.03e-02 8.27e+00 pdb=" CG TYR C 13 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 13 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR C 13 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR C 13 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR C 13 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 13 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 13 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 13 " -0.006 2.00e-02 2.50e+03 2.03e-02 8.26e+00 pdb=" CG TYR E 13 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR E 13 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR E 13 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 13 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR E 13 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 13 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 13 " -0.006 2.00e-02 2.50e+03 2.03e-02 8.23e+00 pdb=" CG TYR B 13 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B 13 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 13 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 13 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 13 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 13 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 13 " 0.002 2.00e-02 2.50e+03 ... (remaining 332 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 632 2.90 - 3.40: 1158 3.40 - 3.90: 2707 3.90 - 4.40: 3087 4.40 - 4.90: 5828 Nonbonded interactions: 13412 Sorted by model distance: nonbonded pdb=" NE2 GLN D 23 " pdb=" OD1 ASN D 27 " model vdw 2.397 3.120 nonbonded pdb=" NE2 GLN E 23 " pdb=" OD1 ASN E 27 " model vdw 2.397 3.120 nonbonded pdb=" NE2 GLN A 23 " pdb=" OD1 ASN A 27 " model vdw 2.397 3.120 nonbonded pdb=" NE2 GLN B 23 " pdb=" OD1 ASN B 27 " model vdw 2.397 3.120 nonbonded pdb=" NE2 GLN C 23 " pdb=" OD1 ASN C 27 " model vdw 2.398 3.120 ... (remaining 13407 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: 0.250 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: 0.020 Check model and map are aligned: 0.020 Set scattering table: 0.000 Process input model: 3.800 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.005 0.035 1660 Z= 0.315 Angle : 0.851 6.417 2225 Z= 0.509 Chirality : 0.048 0.163 170 Planarity : 0.006 0.021 335 Dihedral : 19.930 89.184 615 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % 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 are not related in a simple way. whole: -4.93 (0.20), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.15), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 28 TYR 0.042 0.004 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 1660) covalent geometry : angle 0.85150 ( 2225) hydrogen bonds : bond 0.13881 ( 32) hydrogen bonds : angle 10.86981 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.064 Fit side-chains REVERT: B 28 ARG cc_start: 0.8517 (ttm170) cc_final: 0.8255 (ttp-110) REVERT: C 28 ARG cc_start: 0.8509 (ttm170) cc_final: 0.8204 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0761 time to fit residues: 4.3738 Evaluate side-chains 32 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 3 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: A 9 ASN A 11 GLN A 23 GLN A 48 ASN B 9 ASN B 11 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN C 9 ASN C 11 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN D 11 GLN D 18 GLN D 19 ASN E 9 ASN E 11 GLN E 18 GLN E 23 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.147453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.129832 restraints weight = 2067.792| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.38 r_work: 0.3841 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1660 Z= 0.174 Angle : 0.475 3.028 2225 Z= 0.281 Chirality : 0.034 0.105 170 Planarity : 0.002 0.007 335 Dihedral : 3.612 10.294 225 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.82 % Allowed : 23.64 % Favored : 74.55 % 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: -4.31 (0.22), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.17), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 28 TYR 0.013 0.002 TYR A 13 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 1660) covalent geometry : angle 0.47540 ( 2225) hydrogen bonds : bond 0.02441 ( 32) hydrogen bonds : angle 5.49171 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.065 Fit side-chains REVERT: B 28 ARG cc_start: 0.8396 (ttm170) cc_final: 0.8081 (ttp-170) REVERT: C 28 ARG cc_start: 0.8392 (ttm170) cc_final: 0.8049 (ttp-170) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.0844 time to fit residues: 4.1907 Evaluate side-chains 39 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 0.0270 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.136320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.116720 restraints weight = 2164.352| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.49 r_work: 0.3869 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 1660 Z= 0.280 Angle : 0.511 3.262 2225 Z= 0.300 Chirality : 0.034 0.099 170 Planarity : 0.002 0.011 335 Dihedral : 3.642 10.548 225 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.21 % Allowed : 26.67 % Favored : 72.12 % 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: -4.15 (0.25), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.19), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 28 TYR 0.026 0.002 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 1660) covalent geometry : angle 0.51111 ( 2225) hydrogen bonds : bond 0.02485 ( 32) hydrogen bonds : angle 4.58550 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.061 Fit side-chains REVERT: B 28 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7860 (ttp-170) REVERT: C 4 SER cc_start: 0.7110 (p) cc_final: 0.6833 (p) REVERT: C 28 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7659 (ttp-170) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.0887 time to fit residues: 3.9026 Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 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 = 0.4157 r_free = 0.4157 target = 0.139479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.119981 restraints weight = 2086.801| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.42 r_work: 0.3920 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1660 Z= 0.149 Angle : 0.422 3.083 2225 Z= 0.246 Chirality : 0.035 0.091 170 Planarity : 0.001 0.010 335 Dihedral : 3.181 9.435 225 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.61 % Allowed : 29.09 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.27), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.21), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 28 TYR 0.023 0.002 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 1660) covalent geometry : angle 0.42191 ( 2225) hydrogen bonds : bond 0.01841 ( 32) hydrogen bonds : angle 4.24318 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.067 Fit side-chains REVERT: B 28 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7777 (ttp-170) REVERT: C 4 SER cc_start: 0.7131 (p) cc_final: 0.6821 (p) REVERT: C 28 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7641 (ttp-170) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0980 time to fit residues: 4.0944 Evaluate side-chains 35 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.141785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.122232 restraints weight = 2082.375| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.42 r_work: 0.3956 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 1660 Z= 0.096 Angle : 0.376 2.647 2225 Z= 0.220 Chirality : 0.035 0.084 170 Planarity : 0.001 0.007 335 Dihedral : 2.813 9.493 225 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.61 % Allowed : 32.12 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.27), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 28 TYR 0.017 0.001 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 1660) covalent geometry : angle 0.37599 ( 2225) hydrogen bonds : bond 0.01389 ( 32) hydrogen bonds : angle 4.01559 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.068 Fit side-chains REVERT: B 28 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7788 (ttp-170) REVERT: C 4 SER cc_start: 0.7201 (p) cc_final: 0.6896 (p) REVERT: C 28 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7617 (ttp-170) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.0954 time to fit residues: 4.0909 Evaluate side-chains 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.141209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.122227 restraints weight = 2114.410| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.36 r_work: 0.3910 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1660 Z= 0.150 Angle : 0.405 2.301 2225 Z= 0.238 Chirality : 0.035 0.086 170 Planarity : 0.001 0.008 335 Dihedral : 3.025 10.116 225 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.21 % Allowed : 30.30 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.28), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 28 TYR 0.020 0.001 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 1660) covalent geometry : angle 0.40452 ( 2225) hydrogen bonds : bond 0.01778 ( 32) hydrogen bonds : angle 3.97068 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.083 Fit side-chains REVERT: B 24 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.9108 (mt0) REVERT: B 28 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7863 (ttp-170) REVERT: C 4 SER cc_start: 0.7265 (p) cc_final: 0.6904 (p) REVERT: C 28 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7639 (ttp-170) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.0989 time to fit residues: 4.2337 Evaluate side-chains 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain C residue 48 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.145812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.127532 restraints weight = 2063.296| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.44 r_work: 0.3832 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1660 Z= 0.146 Angle : 0.396 2.258 2225 Z= 0.234 Chirality : 0.035 0.085 170 Planarity : 0.001 0.009 335 Dihedral : 2.992 9.700 225 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.21 % Allowed : 28.48 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.29), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.22), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 28 TYR 0.021 0.002 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 1660) covalent geometry : angle 0.39631 ( 2225) hydrogen bonds : bond 0.01784 ( 32) hydrogen bonds : angle 3.93779 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.063 Fit side-chains REVERT: B 13 TYR cc_start: 0.9481 (m-80) cc_final: 0.9189 (m-80) REVERT: B 24 GLN cc_start: 0.9457 (OUTLIER) cc_final: 0.9150 (mt0) REVERT: B 28 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8097 (ttp-170) REVERT: C 4 SER cc_start: 0.7344 (p) cc_final: 0.7053 (p) REVERT: C 28 ARG cc_start: 0.8345 (ttm170) cc_final: 0.7980 (ttp-170) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.1060 time to fit residues: 4.2832 Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain C residue 48 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 0.0270 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.145420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.126965 restraints weight = 2047.391| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.41 r_work: 0.3841 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1660 Z= 0.137 Angle : 0.389 2.199 2225 Z= 0.230 Chirality : 0.035 0.085 170 Planarity : 0.001 0.008 335 Dihedral : 2.913 9.966 225 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.21 % Allowed : 27.27 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.30), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.23), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 28 TYR 0.019 0.001 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 1660) covalent geometry : angle 0.38947 ( 2225) hydrogen bonds : bond 0.01724 ( 32) hydrogen bonds : angle 3.92020 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.039 Fit side-chains REVERT: B 24 GLN cc_start: 0.9458 (OUTLIER) cc_final: 0.9161 (mt0) REVERT: B 28 ARG cc_start: 0.8408 (ttm170) cc_final: 0.8093 (ttp-170) REVERT: C 4 SER cc_start: 0.7326 (p) cc_final: 0.7054 (p) REVERT: C 28 ARG cc_start: 0.8355 (ttm170) cc_final: 0.7993 (ttp-170) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.0780 time to fit residues: 3.3389 Evaluate side-chains 39 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain C residue 48 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.144896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.126544 restraints weight = 2076.493| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.40 r_work: 0.3787 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1660 Z= 0.157 Angle : 0.402 2.330 2225 Z= 0.238 Chirality : 0.035 0.084 170 Planarity : 0.002 0.009 335 Dihedral : 3.003 9.954 225 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.42 % Allowed : 26.06 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.31), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.23), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 28 TYR 0.021 0.002 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 1660) covalent geometry : angle 0.40246 ( 2225) hydrogen bonds : bond 0.01817 ( 32) hydrogen bonds : angle 3.92890 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.063 Fit side-chains REVERT: B 13 TYR cc_start: 0.9474 (m-80) cc_final: 0.9243 (m-80) REVERT: B 24 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.9172 (mt0) REVERT: B 28 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8070 (ttp-170) REVERT: C 4 SER cc_start: 0.7368 (p) cc_final: 0.7079 (p) REVERT: C 28 ARG cc_start: 0.8287 (ttm170) cc_final: 0.7820 (ttp-170) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.0566 time to fit residues: 2.5933 Evaluate side-chains 39 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain C residue 48 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.142601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.124183 restraints weight = 2122.957| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.41 r_work: 0.3757 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 1660 Z= 0.255 Angle : 0.461 2.601 2225 Z= 0.272 Chirality : 0.034 0.088 170 Planarity : 0.002 0.011 335 Dihedral : 3.230 9.787 225 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.21 % Allowed : 27.27 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.31), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.24), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.027 0.002 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 1660) covalent geometry : angle 0.46061 ( 2225) hydrogen bonds : bond 0.02379 ( 32) hydrogen bonds : angle 4.07557 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 350 Ramachandran restraints generated. 175 Oldfield, 0 Emsley, 175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.037 Fit side-chains REVERT: A 13 TYR cc_start: 0.9505 (m-80) cc_final: 0.9251 (m-80) REVERT: B 24 GLN cc_start: 0.9475 (OUTLIER) cc_final: 0.9205 (mt0) REVERT: B 28 ARG cc_start: 0.8385 (ttm170) cc_final: 0.8076 (ttp-170) REVERT: C 4 SER cc_start: 0.7267 (p) cc_final: 0.6981 (p) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.0454 time to fit residues: 2.0406 Evaluate side-chains 39 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain C residue 48 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.126812 restraints weight = 2102.458| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.51 r_work: 0.3799 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1660 Z= 0.148 Angle : 0.400 2.266 2225 Z= 0.236 Chirality : 0.035 0.087 170 Planarity : 0.001 0.008 335 Dihedral : 2.956 9.743 225 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.82 % Allowed : 26.67 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.31), residues: 175 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.23), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 28 TYR 0.020 0.002 TYR B 13 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 1660) covalent geometry : angle 0.39996 ( 2225) hydrogen bonds : bond 0.01856 ( 32) hydrogen bonds : angle 3.96026 ( 96) =============================================================================== Job complete usr+sys time: 655.10 seconds wall clock time: 12 minutes 14.50 seconds (734.50 seconds total)