Starting phenix.real_space_refine on Wed Sep 17 02:57:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qjp_4565/09_2025/6qjp_4565.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qjp_4565/09_2025/6qjp_4565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qjp_4565/09_2025/6qjp_4565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qjp_4565/09_2025/6qjp_4565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qjp_4565/09_2025/6qjp_4565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qjp_4565/09_2025/6qjp_4565.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 522 2.51 5 N 141 2.21 5 O 153 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 816 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 272 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 0.16, per 1000 atoms: 0.20 Number of scatterers: 816 At special positions: 0 Unit cell: (52.44, 69, 37.26, 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 153 8.00 N 141 7.00 C 522 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: 0.03 Conformation dependent library (CDL) restraints added in 17.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 204 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 62.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 288 removed outlier: 6.132A pdb=" N GLN A 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN C 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS C 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS A 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP C 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU A 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER C 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 284 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL C 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN A 286 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.448A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 318 removed outlier: 6.011A pdb=" N ASP A 314 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS C 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER A 316 " --> pdb=" O LYS C 317 " (cutoff:3.500A) 22 hydrogen bonds defined for protein. 66 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: 0.05 Time building geometry restraints manager: 0.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 132 1.29 - 1.35: 114 1.35 - 1.42: 33 1.42 - 1.48: 123 1.48 - 1.55: 414 Bond restraints: 816 Sorted by residual: bond pdb=" CG1 ILE B 278 " pdb=" CD1 ILE B 278 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 3.98e+00 bond pdb=" CG1 ILE A 278 " pdb=" CD1 ILE A 278 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 3.97e+00 bond pdb=" CG1 ILE C 278 " pdb=" CD1 ILE C 278 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 bond pdb=" CA SER A 320 " pdb=" CB SER A 320 " ideal model delta sigma weight residual 1.535 1.510 0.025 1.90e-02 2.77e+03 1.70e+00 bond pdb=" CA SER C 320 " pdb=" CB SER C 320 " ideal model delta sigma weight residual 1.535 1.511 0.024 1.90e-02 2.77e+03 1.64e+00 ... (remaining 811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 1003 1.41 - 2.83: 59 2.83 - 4.24: 12 4.24 - 5.66: 9 5.66 - 7.07: 3 Bond angle restraints: 1086 Sorted by residual: angle pdb=" C THR B 319 " pdb=" CA THR B 319 " pdb=" CB THR B 319 " ideal model delta sigma weight residual 110.30 103.23 7.07 1.98e+00 2.55e-01 1.28e+01 angle pdb=" C THR A 319 " pdb=" CA THR A 319 " pdb=" CB THR A 319 " ideal model delta sigma weight residual 110.30 103.25 7.05 1.98e+00 2.55e-01 1.27e+01 angle pdb=" C THR C 319 " pdb=" CA THR C 319 " pdb=" CB THR C 319 " ideal model delta sigma weight residual 110.30 103.25 7.05 1.98e+00 2.55e-01 1.27e+01 angle pdb=" CA TYR A 310 " pdb=" CB TYR A 310 " pdb=" CG TYR A 310 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.58e+00 angle pdb=" CA TYR C 310 " pdb=" CB TYR C 310 " pdb=" CG TYR C 310 " ideal model delta sigma weight residual 113.90 118.48 -4.58 1.80e+00 3.09e-01 6.48e+00 ... (remaining 1081 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 5.21: 339 5.21 - 10.41: 94 10.41 - 15.61: 65 15.61 - 20.80: 21 20.80 - 26.00: 9 Dihedral angle restraints: 528 sinusoidal: 222 harmonic: 306 Sorted by residual: dihedral pdb=" C THR B 319 " pdb=" N THR B 319 " pdb=" CA THR B 319 " pdb=" CB THR B 319 " ideal model delta harmonic sigma weight residual -122.00 -113.14 -8.86 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" C THR A 319 " pdb=" N THR A 319 " pdb=" CA THR A 319 " pdb=" CB THR A 319 " ideal model delta harmonic sigma weight residual -122.00 -113.19 -8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C THR C 319 " pdb=" N THR C 319 " pdb=" CA THR C 319 " pdb=" CB THR C 319 " ideal model delta harmonic sigma weight residual -122.00 -113.19 -8.81 0 2.50e+00 1.60e-01 1.24e+01 ... (remaining 525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 65 0.037 - 0.074: 46 0.074 - 0.111: 18 0.111 - 0.149: 9 0.149 - 0.186: 3 Chirality restraints: 141 Sorted by residual: chirality pdb=" CA THR B 319 " pdb=" N THR B 319 " pdb=" C THR B 319 " pdb=" CB THR B 319 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA THR C 319 " pdb=" N THR C 319 " pdb=" C THR C 319 " pdb=" CB THR C 319 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA THR A 319 " pdb=" N THR A 319 " pdb=" C THR A 319 " pdb=" CB THR A 319 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 138 not shown) Planarity restraints: 126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.036 2.00e-02 2.50e+03 1.94e-02 7.52e+00 pdb=" CG TYR C 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.036 2.00e-02 2.50e+03 1.94e-02 7.50e+00 pdb=" CG TYR B 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.036 2.00e-02 2.50e+03 1.93e-02 7.44e+00 pdb=" CG TYR A 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.012 2.00e-02 2.50e+03 ... (remaining 123 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.06: 452 3.06 - 3.52: 777 3.52 - 3.98: 1135 3.98 - 4.44: 989 4.44 - 4.90: 2318 Nonbonded interactions: 5671 Sorted by model distance: nonbonded pdb=" C THR B 319 " pdb=" OG1 THR B 319 " model vdw 2.605 2.616 nonbonded pdb=" C THR A 319 " pdb=" OG1 THR A 319 " model vdw 2.606 2.616 nonbonded pdb=" C THR C 319 " pdb=" OG1 THR C 319 " model vdw 2.606 2.616 nonbonded pdb=" N THR C 319 " pdb=" O THR C 319 " model vdw 2.646 2.496 nonbonded pdb=" N THR A 319 " pdb=" O THR A 319 " model vdw 2.646 2.496 ... (remaining 5666 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.000 Set scattering table: 0.000 Process input model: 1.970 Find NCS groups from input model: 0.000 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:0.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.009 0.078 816 Z= 0.414 Angle : 1.011 7.071 1086 Z= 0.536 Chirality : 0.065 0.186 141 Planarity : 0.007 0.036 126 Dihedral : 9.521 26.002 324 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.78), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.60), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.036 0.015 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00927 ( 816) covalent geometry : angle 1.01089 ( 1086) hydrogen bonds : bond 0.20502 ( 22) hydrogen bonds : angle 10.51405 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.020 Fit side-chains REVERT: A 288 GLN cc_start: 0.7303 (mt0) cc_final: 0.6987 (mt0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0256 time to fit residues: 0.8324 Evaluate side-chains 14 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 1.1733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 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 = 0.4354 r_free = 0.4354 target = 0.143049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.122145 restraints weight = 1214.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.126215 restraints weight = 530.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.129060 restraints weight = 321.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.130761 restraints weight = 231.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.131931 restraints weight = 188.167| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 816 Z= 0.129 Angle : 0.621 4.679 1086 Z= 0.318 Chirality : 0.052 0.132 141 Planarity : 0.005 0.031 126 Dihedral : 6.382 16.861 102 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.94 % Allowed : 7.84 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.81), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.62), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.004 TYR A 310 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 816) covalent geometry : angle 0.62091 ( 1086) hydrogen bonds : bond 0.02974 ( 22) hydrogen bonds : angle 6.22701 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.020 Fit side-chains REVERT: A 276 GLN cc_start: 0.7102 (mt0) cc_final: 0.6839 (mp10) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.0119 time to fit residues: 0.3358 Evaluate side-chains 17 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 overall best weight: 1.3735 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.135171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.114467 restraints weight = 1193.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.117945 restraints weight = 520.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.120143 restraints weight = 320.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.121673 restraints weight = 238.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.122762 restraints weight = 195.873| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 816 Z= 0.134 Angle : 0.622 4.822 1086 Z= 0.314 Chirality : 0.050 0.129 141 Planarity : 0.004 0.023 126 Dihedral : 6.399 17.045 102 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.92 % Allowed : 9.80 % Favored : 86.27 % 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 aren not related in a simple way. whole: -2.65 (0.78), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 816) covalent geometry : angle 0.62224 ( 1086) hydrogen bonds : bond 0.02426 ( 22) hydrogen bonds : angle 5.62911 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.020 Fit side-chains REVERT: A 276 GLN cc_start: 0.7132 (mt0) cc_final: 0.6857 (mp10) REVERT: B 278 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8316 (mt) outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 0.0120 time to fit residues: 0.3117 Evaluate side-chains 20 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain B residue 278 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.131258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.110760 restraints weight = 1271.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.114228 restraints weight = 594.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.116495 restraints weight = 380.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.117882 restraints weight = 287.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.118930 restraints weight = 240.443| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 816 Z= 0.200 Angle : 0.705 5.549 1086 Z= 0.361 Chirality : 0.051 0.125 141 Planarity : 0.003 0.015 126 Dihedral : 6.761 18.351 102 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.94 % Allowed : 11.76 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.74), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.006 TYR B 310 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 816) covalent geometry : angle 0.70487 ( 1086) hydrogen bonds : bond 0.02493 ( 22) hydrogen bonds : angle 5.77306 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.020 Fit side-chains REVERT: A 276 GLN cc_start: 0.7301 (mt0) cc_final: 0.6993 (mp10) REVERT: B 278 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8405 (mt) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.0117 time to fit residues: 0.2896 Evaluate side-chains 19 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain B residue 278 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 1.1985 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.135144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.114281 restraints weight = 1247.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.117837 restraints weight = 546.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.120132 restraints weight = 335.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.121700 restraints weight = 247.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.122717 restraints weight = 202.389| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 816 Z= 0.119 Angle : 0.611 4.268 1086 Z= 0.308 Chirality : 0.051 0.125 141 Planarity : 0.002 0.013 126 Dihedral : 6.331 17.242 102 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 8.82 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.75), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 816) covalent geometry : angle 0.61127 ( 1086) hydrogen bonds : bond 0.02034 ( 22) hydrogen bonds : angle 5.27133 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.020 Fit side-chains REVERT: A 276 GLN cc_start: 0.7111 (mt0) cc_final: 0.6806 (mp10) REVERT: B 278 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8254 (mt) outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 0.0130 time to fit residues: 0.3193 Evaluate side-chains 20 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 278 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.138298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.116943 restraints weight = 1182.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.120786 restraints weight = 517.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.123303 restraints weight = 313.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.124949 restraints weight = 227.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.125681 restraints weight = 184.343| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 816 Z= 0.087 Angle : 0.557 3.936 1086 Z= 0.279 Chirality : 0.051 0.123 141 Planarity : 0.002 0.011 126 Dihedral : 5.928 15.840 102 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 11.76 % Favored : 86.27 % 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 aren not related in a simple way. whole: -2.92 (0.76), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.58), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 816) covalent geometry : angle 0.55651 ( 1086) hydrogen bonds : bond 0.01670 ( 22) hydrogen bonds : angle 4.84296 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.020 Fit side-chains REVERT: A 276 GLN cc_start: 0.7028 (mt0) cc_final: 0.6751 (mp10) outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 0.0122 time to fit residues: 0.3164 Evaluate side-chains 19 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.134337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.113025 restraints weight = 1203.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.116368 restraints weight = 536.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.118556 restraints weight = 336.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.120184 restraints weight = 254.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.121202 restraints weight = 208.586| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 816 Z= 0.155 Angle : 0.647 4.710 1086 Z= 0.329 Chirality : 0.051 0.122 141 Planarity : 0.002 0.010 126 Dihedral : 6.266 16.464 102 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.94 % Allowed : 12.75 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.75), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.005 TYR B 310 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 816) covalent geometry : angle 0.64729 ( 1086) hydrogen bonds : bond 0.02125 ( 22) hydrogen bonds : angle 5.13270 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.020 Fit side-chains REVERT: A 276 GLN cc_start: 0.7145 (mt0) cc_final: 0.6817 (mp10) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.0136 time to fit residues: 0.3175 Evaluate side-chains 19 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.137878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.116374 restraints weight = 1191.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.119960 restraints weight = 527.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.122328 restraints weight = 326.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.124028 restraints weight = 241.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.125134 restraints weight = 196.902| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 816 Z= 0.094 Angle : 0.582 4.090 1086 Z= 0.291 Chirality : 0.051 0.123 141 Planarity : 0.002 0.010 126 Dihedral : 5.968 15.573 102 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 11.76 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.97 (0.75), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.004 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 816) covalent geometry : angle 0.58164 ( 1086) hydrogen bonds : bond 0.01830 ( 22) hydrogen bonds : angle 4.82163 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.021 Fit side-chains REVERT: A 276 GLN cc_start: 0.7102 (mt0) cc_final: 0.6824 (mp10) outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 0.0128 time to fit residues: 0.3030 Evaluate side-chains 21 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.135865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.114501 restraints weight = 1220.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.117964 restraints weight = 547.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.120034 restraints weight = 339.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.121562 restraints weight = 261.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.122517 restraints weight = 217.389| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 816 Z= 0.154 Angle : 0.652 4.817 1086 Z= 0.331 Chirality : 0.051 0.124 141 Planarity : 0.002 0.010 126 Dihedral : 6.242 16.269 102 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.90 % Allowed : 10.78 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.74), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.005 TYR A 310 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 816) covalent geometry : angle 0.65246 ( 1086) hydrogen bonds : bond 0.02133 ( 22) hydrogen bonds : angle 5.07960 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.042 Fit side-chains REVERT: A 276 GLN cc_start: 0.7166 (mt0) cc_final: 0.6851 (mp10) REVERT: C 288 GLN cc_start: 0.8202 (mt0) cc_final: 0.7893 (mp10) outliers start: 5 outliers final: 5 residues processed: 18 average time/residue: 0.0255 time to fit residues: 0.5863 Evaluate side-chains 22 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 1.5985 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.134621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.112872 restraints weight = 1190.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.116311 restraints weight = 537.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.118499 restraints weight = 338.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.120043 restraints weight = 255.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.121071 restraints weight = 213.430| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 816 Z= 0.144 Angle : 0.642 4.781 1086 Z= 0.326 Chirality : 0.051 0.124 141 Planarity : 0.002 0.009 126 Dihedral : 6.215 16.459 102 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.90 % Allowed : 10.78 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.74), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.005 TYR A 310 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 816) covalent geometry : angle 0.64230 ( 1086) hydrogen bonds : bond 0.02136 ( 22) hydrogen bonds : angle 5.07315 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.038 Fit side-chains REVERT: A 276 GLN cc_start: 0.7177 (mt0) cc_final: 0.6874 (mp10) REVERT: C 288 GLN cc_start: 0.8198 (mt0) cc_final: 0.7896 (mp10) outliers start: 5 outliers final: 5 residues processed: 18 average time/residue: 0.0243 time to fit residues: 0.5597 Evaluate side-chains 22 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.139406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.117730 restraints weight = 1168.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.121412 restraints weight = 514.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.123880 restraints weight = 317.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.125470 restraints weight = 233.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.126655 restraints weight = 191.422| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 816 Z= 0.083 Angle : 0.570 4.094 1086 Z= 0.286 Chirality : 0.051 0.122 141 Planarity : 0.002 0.008 126 Dihedral : 5.869 15.508 102 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 11.76 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.97 (0.74), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.004 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 816) covalent geometry : angle 0.57034 ( 1086) hydrogen bonds : bond 0.01703 ( 22) hydrogen bonds : angle 4.66024 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 303.21 seconds wall clock time: 5 minutes 55.04 seconds (355.04 seconds total)