Starting phenix.real_space_refine on Tue Aug 4 11:46:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbp_61322/08_2026/9jbp_61322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbp_61322/08_2026/9jbp_61322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jbp_61322/08_2026/9jbp_61322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbp_61322/08_2026/9jbp_61322_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jbp_61322/08_2026/9jbp_61322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbp_61322/08_2026/9jbp_61322.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 1278 2.51 5 N 354 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2022 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 297 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, C, D, E, F, H, I, J, K, L Time building chain proxies: 0.68, per 1000 atoms: 0.34 Number of scatterers: 2022 At special positions: 0 Unit cell: (68.04, 103.68, 32.4, 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 390 8.00 N 354 7.00 C 1278 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: 0.14 Conformation dependent library (CDL) restraints added in 71.8 milliseconds 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.517A pdb=" N GLN A 15 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN B 15 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 17 " --> pdb=" O ILE C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.174A pdb=" N VAL B 31 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER C 34 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B 33 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 6 removed outlier: 5.947A pdb=" N UNK G 4 " --> pdb=" O UNK H 5 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N UNK H 4 " --> pdb=" O UNK I 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AA6, first strand: chain 'D' and resid 14 through 18 removed outlier: 5.667A pdb=" N GLN D 15 " --> pdb=" O GLY E 16 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE E 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 17 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN E 15 " --> pdb=" O GLY F 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE F 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 17 " --> pdb=" O ILE F 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 35 removed outlier: 6.410A pdb=" N VAL D 31 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER E 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY D 33 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL E 31 " --> pdb=" O TRP F 32 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER F 34 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY E 33 " --> pdb=" O SER F 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.044A pdb=" N UNK J 4 " --> pdb=" O UNK K 5 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N UNK K 4 " --> pdb=" O UNK L 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 20 hydrogen bonds defined for protein. 60 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.27 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 366 1.29 - 1.35: 306 1.35 - 1.42: 102 1.42 - 1.48: 324 1.48 - 1.54: 942 Bond restraints: 2040 Sorted by residual: bond pdb=" CB VAL E 29 " pdb=" CG1 VAL E 29 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.63e-01 bond pdb=" CB VAL A 29 " pdb=" CG1 VAL A 29 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.57e-01 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.45e-01 bond pdb=" CB VAL B 29 " pdb=" CG1 VAL B 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.40e-01 bond pdb=" CB VAL D 29 " pdb=" CG1 VAL D 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.39e-01 ... (remaining 2035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2615 1.44 - 2.89: 121 2.89 - 4.33: 6 4.33 - 5.78: 0 5.78 - 7.22: 6 Bond angle restraints: 2748 Sorted by residual: angle pdb=" CA LEU D 38 " pdb=" CB LEU D 38 " pdb=" CG LEU D 38 " ideal model delta sigma weight residual 116.30 123.52 -7.22 3.50e+00 8.16e-02 4.25e+00 angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.24e+00 angle pdb=" CA LEU E 38 " pdb=" CB LEU E 38 " pdb=" CG LEU E 38 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 123.49 -7.19 3.50e+00 8.16e-02 4.23e+00 angle pdb=" CA LEU F 38 " pdb=" CB LEU F 38 " pdb=" CG LEU F 38 " ideal model delta sigma weight residual 116.30 123.49 -7.19 3.50e+00 8.16e-02 4.22e+00 ... (remaining 2743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 1052 15.81 - 31.63: 112 31.63 - 47.44: 18 47.44 - 63.26: 18 63.26 - 79.07: 6 Dihedral angle restraints: 1206 sinusoidal: 420 harmonic: 786 Sorted by residual: dihedral pdb=" CA GLN C 15 " pdb=" CB GLN C 15 " pdb=" CG GLN C 15 " pdb=" CD GLN C 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.88 37.12 3 1.50e+01 4.44e-03 6.47e+00 dihedral pdb=" CA GLN F 15 " pdb=" CB GLN F 15 " pdb=" CG GLN F 15 " pdb=" CD GLN F 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.88 37.12 3 1.50e+01 4.44e-03 6.47e+00 dihedral pdb=" CA GLN B 15 " pdb=" CB GLN B 15 " pdb=" CG GLN B 15 " pdb=" CD GLN B 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.89 37.11 3 1.50e+01 4.44e-03 6.47e+00 ... (remaining 1203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 168 0.030 - 0.060: 99 0.060 - 0.091: 9 0.091 - 0.121: 42 0.121 - 0.151: 6 Chirality restraints: 324 Sorted by residual: chirality pdb=" CG LEU A 38 " pdb=" CB LEU A 38 " pdb=" CD1 LEU A 38 " pdb=" CD2 LEU A 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CG LEU F 38 " pdb=" CB LEU F 38 " pdb=" CD1 LEU F 38 " pdb=" CD2 LEU F 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CG LEU E 38 " pdb=" CB LEU E 38 " pdb=" CD1 LEU E 38 " pdb=" CD2 LEU E 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 321 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 12 " -0.010 5.00e-02 4.00e+02 1.50e-02 3.58e-01 pdb=" N PRO B 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO B 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO B 13 " -0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 12 " -0.010 5.00e-02 4.00e+02 1.49e-02 3.57e-01 pdb=" N PRO E 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO E 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO E 13 " -0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 12 " -0.010 5.00e-02 4.00e+02 1.48e-02 3.49e-01 pdb=" N PRO F 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO F 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO F 13 " -0.008 5.00e-02 4.00e+02 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 897 2.92 - 3.41: 1607 3.41 - 3.91: 3159 3.91 - 4.40: 3013 4.40 - 4.90: 6557 Nonbonded interactions: 15233 Sorted by model distance: nonbonded pdb=" ND2 ASN B 26 " pdb=" O ASN C 26 " model vdw 2.424 3.120 nonbonded pdb=" O ALA A 1 " pdb=" N ALA B 1 " model vdw 2.463 3.120 nonbonded pdb=" O ALA D 1 " pdb=" N ALA E 1 " model vdw 2.482 3.120 nonbonded pdb=" ND2 ASN D 26 " pdb=" O ASN E 26 " model vdw 2.514 3.120 nonbonded pdb=" ND2 ASN E 26 " pdb=" O ASN F 26 " model vdw 2.515 3.120 ... (remaining 15228 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' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.790 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 0.003 0.020 2040 Z= 0.137 Angle : 0.697 7.219 2748 Z= 0.346 Chirality : 0.051 0.151 324 Planarity : 0.003 0.015 354 Dihedral : 16.942 79.069 702 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 25.81 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.57), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.52 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.002 PHE C 20 TRP 0.002 0.000 TRP C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 2040) covalent geometry : angle 0.69663 / 0.35 ( 2748) hydrogen bonds : bond 0.14889 / 8.65 ( 20) hydrogen bonds : angle 8.20527 / 5.32 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0274 time to fit residues: 1.0330 Evaluate side-chains 25 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 ASN B 26 ASN C 26 ASN D 26 ASN E 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6043 r_free = 0.6043 target = 0.398150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.6231 r_free = 0.6231 target = 0.360271 restraints weight = 2573.062| |-----------------------------------------------------------------------------| r_work (start): 0.5503 rms_B_bonded: 1.58 r_work: 0.5353 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.5251 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.5251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2040 Z= 0.306 Angle : 0.746 5.841 2748 Z= 0.394 Chirality : 0.048 0.116 324 Planarity : 0.005 0.030 354 Dihedral : 4.365 13.617 282 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 8.06 % Allowed : 21.51 % Favored : 70.43 % 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: -0.96 (0.55), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 20 TRP 0.015 0.003 TRP E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.31 ( 2040) covalent geometry : angle 0.74589 / 0.39 ( 2748) hydrogen bonds : bond 0.04449 / 2.47 ( 20) hydrogen bonds : angle 5.34496 / 3.51 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.076 Fit side-chains REVERT: F 24 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7602 (tt0) outliers start: 15 outliers final: 14 residues processed: 44 average time/residue: 0.0240 time to fit residues: 1.5014 Evaluate side-chains 48 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 GLN B 26 ASN C 15 GLN C 26 ASN D 26 ASN E 15 GLN E 26 ASN F 15 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6119 r_free = 0.6119 target = 0.449524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.6422 r_free = 0.6422 target = 0.378701 restraints weight = 2777.260| |-----------------------------------------------------------------------------| r_work (start): 0.5648 rms_B_bonded: 1.55 r_work: 0.5516 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.5421 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.5421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2040 Z= 0.110 Angle : 0.488 3.873 2748 Z= 0.256 Chirality : 0.045 0.117 324 Planarity : 0.003 0.021 354 Dihedral : 3.304 10.505 282 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.84 % Allowed : 24.19 % Favored : 70.97 % 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: -1.03 (0.54), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE E 20 TRP 0.005 0.001 TRP B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 2040) covalent geometry : angle 0.48837 / 0.26 ( 2748) hydrogen bonds : bond 0.02615 / 1.48 ( 20) hydrogen bonds : angle 4.38562 / 2.90 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.071 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.0296 time to fit residues: 1.5812 Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN C 26 ASN D 26 ASN E 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6001 r_free = 0.6001 target = 0.398613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.6179 r_free = 0.6179 target = 0.358641 restraints weight = 2578.323| |-----------------------------------------------------------------------------| r_work (start): 0.5491 rms_B_bonded: 1.64 r_work: 0.5330 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.5231 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.5231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2040 Z= 0.270 Angle : 0.675 4.472 2748 Z= 0.362 Chirality : 0.047 0.125 324 Planarity : 0.004 0.028 354 Dihedral : 4.310 12.933 282 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 10.22 % Allowed : 22.04 % Favored : 67.74 % 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: -1.27 (0.52), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE F 20 TRP 0.013 0.003 TRP A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 ( 2040) covalent geometry : angle 0.67542 / 0.36 ( 2748) hydrogen bonds : bond 0.03347 / 1.80 ( 20) hydrogen bonds : angle 4.53058 / 3.01 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.075 Fit side-chains REVERT: F 24 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7610 (tt0) outliers start: 19 outliers final: 16 residues processed: 46 average time/residue: 0.0360 time to fit residues: 2.1417 Evaluate side-chains 47 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.0010 chunk 22 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN C 26 ASN D 26 ASN E 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6074 r_free = 0.6074 target = 0.410411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.6266 r_free = 0.6266 target = 0.372286 restraints weight = 2589.567| |-----------------------------------------------------------------------------| r_work (start): 0.5626 rms_B_bonded: 1.67 r_work: 0.5489 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.5389 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.5389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2040 Z= 0.106 Angle : 0.500 4.428 2748 Z= 0.266 Chirality : 0.045 0.120 324 Planarity : 0.003 0.019 354 Dihedral : 3.367 10.571 282 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.38 % Allowed : 26.88 % Favored : 67.74 % 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: -1.34 (0.51), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE E 20 TRP 0.004 0.001 TRP F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 2040) covalent geometry : angle 0.50025 / 0.27 ( 2748) hydrogen bonds : bond 0.02046 / 1.16 ( 20) hydrogen bonds : angle 4.07292 / 2.69 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.073 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 33 average time/residue: 0.0241 time to fit residues: 1.1621 Evaluate side-chains 38 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 0.0980 chunk 8 optimal weight: 0.0060 chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 9 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.1146 > 50:) chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6034 r_free = 0.6034 target = 0.406663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.6232 r_free = 0.6232 target = 0.367320 restraints weight = 2561.081| |-----------------------------------------------------------------------------| r_work (start): 0.5577 rms_B_bonded: 1.65 r_work: 0.5425 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.5334 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.5334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2040 Z= 0.144 Angle : 0.522 3.894 2748 Z= 0.278 Chirality : 0.045 0.118 324 Planarity : 0.003 0.019 354 Dihedral : 3.554 11.518 282 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 8.06 % Allowed : 25.81 % Favored : 66.13 % 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: -1.45 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.002 PHE F 20 TRP 0.007 0.002 TRP F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 2040) covalent geometry : angle 0.52232 / 0.28 ( 2748) hydrogen bonds : bond 0.02261 / 1.26 ( 20) hydrogen bonds : angle 4.05647 / 2.69 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.078 Fit side-chains REVERT: A 3 LYS cc_start: 0.7806 (mptt) cc_final: 0.6985 (tttt) outliers start: 15 outliers final: 13 residues processed: 42 average time/residue: 0.0410 time to fit residues: 2.1613 Evaluate side-chains 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6013 r_free = 0.6013 target = 0.403811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.6209 r_free = 0.6209 target = 0.362611 restraints weight = 2576.142| |-----------------------------------------------------------------------------| r_work (start): 0.5717 rms_B_bonded: 1.66 r_work: 0.5723 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.5654 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.5654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2040 Z= 0.158 Angle : 0.555 4.623 2748 Z= 0.295 Chirality : 0.046 0.119 324 Planarity : 0.003 0.021 354 Dihedral : 3.703 11.570 282 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.60 % Allowed : 26.34 % Favored : 65.05 % 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: -1.55 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE F 20 TRP 0.008 0.002 TRP A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 2040) covalent geometry : angle 0.55487 / 0.30 ( 2748) hydrogen bonds : bond 0.02378 / 1.34 ( 20) hydrogen bonds : angle 4.07311 / 2.70 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.073 Fit side-chains REVERT: A 3 LYS cc_start: 0.7942 (mptt) cc_final: 0.7180 (tttt) outliers start: 16 outliers final: 14 residues processed: 41 average time/residue: 0.0333 time to fit residues: 1.7775 Evaluate side-chains 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6013 r_free = 0.6013 target = 0.405226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.6208 r_free = 0.6208 target = 0.364139 restraints weight = 2587.603| |-----------------------------------------------------------------------------| r_work (start): 0.5720 rms_B_bonded: 1.64 r_work: 0.5731 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.5668 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.5668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2040 Z= 0.148 Angle : 0.540 4.183 2748 Z= 0.288 Chirality : 0.046 0.120 324 Planarity : 0.003 0.019 354 Dihedral : 3.643 10.735 282 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 9.14 % Allowed : 26.88 % Favored : 63.98 % 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: -1.58 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE F 20 TRP 0.007 0.002 TRP F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 2040) covalent geometry : angle 0.54027 / 0.29 ( 2748) hydrogen bonds : bond 0.02319 / 1.31 ( 20) hydrogen bonds : angle 4.04568 / 2.68 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.069 Fit side-chains REVERT: A 3 LYS cc_start: 0.7949 (mptt) cc_final: 0.7163 (tttt) outliers start: 17 outliers final: 15 residues processed: 42 average time/residue: 0.0365 time to fit residues: 1.9556 Evaluate side-chains 45 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6073 r_free = 0.6073 target = 0.448613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.6392 r_free = 0.6392 target = 0.375971 restraints weight = 2751.114| |-----------------------------------------------------------------------------| r_work (start): 0.5933 rms_B_bonded: 1.50 r_work: 0.6226 rms_B_bonded: 0.85 restraints_weight: 0.5000 r_work: 0.6184 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.5976 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.5976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2040 Z= 0.105 Angle : 0.497 4.671 2748 Z= 0.265 Chirality : 0.045 0.118 324 Planarity : 0.003 0.017 354 Dihedral : 3.189 9.959 282 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.60 % Allowed : 27.96 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE E 20 TRP 0.004 0.001 TRP F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 2040) covalent geometry : angle 0.49698 / 0.26 ( 2748) hydrogen bonds : bond 0.01821 / 1.07 ( 20) hydrogen bonds : angle 3.78098 / 2.49 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.073 Fit side-chains REVERT: E 3 LYS cc_start: 0.8194 (mptt) cc_final: 0.7760 (ttmt) outliers start: 16 outliers final: 14 residues processed: 40 average time/residue: 0.0411 time to fit residues: 2.0792 Evaluate side-chains 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 0.0970 chunk 14 optimal weight: 0.0570 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5992 r_free = 0.5992 target = 0.405564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.6196 r_free = 0.6196 target = 0.362444 restraints weight = 2630.949| |-----------------------------------------------------------------------------| r_work (start): 0.5734 rms_B_bonded: 1.67 r_work: 0.5740 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.5677 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.5677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2040 Z= 0.148 Angle : 0.525 4.297 2748 Z= 0.279 Chirality : 0.046 0.120 324 Planarity : 0.003 0.017 354 Dihedral : 3.515 10.944 282 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.06 % Allowed : 28.49 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.49), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE F 20 TRP 0.008 0.002 TRP B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 2040) covalent geometry : angle 0.52533 / 0.28 ( 2748) hydrogen bonds : bond 0.02147 / 1.21 ( 20) hydrogen bonds : angle 3.91972 / 2.59 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.088 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 40 average time/residue: 0.0391 time to fit residues: 2.0311 Evaluate side-chains 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6036 r_free = 0.6036 target = 0.410097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.6236 r_free = 0.6236 target = 0.368564 restraints weight = 2625.122| |-----------------------------------------------------------------------------| r_work (start): 0.5787 rms_B_bonded: 1.68 r_work: 0.5793 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.5719 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.5719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2040 Z= 0.097 Angle : 0.490 4.882 2748 Z= 0.261 Chirality : 0.045 0.119 324 Planarity : 0.003 0.016 354 Dihedral : 3.040 9.759 282 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.45 % Allowed : 29.57 % Favored : 63.98 % 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: -1.59 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE E 20 TRP 0.004 0.001 TRP F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 2040) covalent geometry : angle 0.49044 / 0.26 ( 2748) hydrogen bonds : bond 0.01681 / 0.99 ( 20) hydrogen bonds : angle 3.71449 / 2.43 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 821.01 seconds wall clock time: 14 minutes 42.89 seconds (882.89 seconds total)