Starting phenix.real_space_refine on Tue Mar 3 12:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cz6_30507/03_2026/7cz6_30507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cz6_30507/03_2026/7cz6_30507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cz6_30507/03_2026/7cz6_30507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cz6_30507/03_2026/7cz6_30507.map" model { file = "/net/cci-nas-00/data/ceres_data/7cz6_30507/03_2026/7cz6_30507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cz6_30507/03_2026/7cz6_30507.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2900 2.51 5 N 700 2.21 5 O 915 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4535 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 116} Restraints were copied for chains: A, B, D, E Time building chain proxies: 0.68, per 1000 atoms: 0.15 Number of scatterers: 4535 At special positions: 0 Unit cell: (71.94, 71.94, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 915 8.00 N 700 7.00 C 2900 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: 0.38 Conformation dependent library (CDL) restraints added in 211.0 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=1, first strand: chain 'C' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR C 275 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 318 " --> pdb=" O TYR C 275 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=3, first strand: chain 'A' and resid 248 through 254 removed outlier: 5.248A pdb=" N TYR A 275 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 318 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 262 through 264 Processing sheet with id=5, first strand: chain 'B' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR B 275 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 318 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=7, first strand: chain 'D' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR D 275 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 318 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 262 through 264 Processing sheet with id=9, first strand: chain 'E' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR E 275 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E 318 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 262 through 264 150 hydrogen bonds defined for protein. 405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1362 1.34 - 1.46: 960 1.46 - 1.58: 2288 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4640 Sorted by residual: bond pdb=" CA PRO E 269 " pdb=" C PRO E 269 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.45e+00 bond pdb=" CA PRO B 269 " pdb=" C PRO B 269 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.43e+00 bond pdb=" CA PRO C 269 " pdb=" C PRO C 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.38e+00 bond pdb=" CA PRO D 269 " pdb=" C PRO D 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.37e+00 bond pdb=" CA PRO A 269 " pdb=" C PRO A 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.37e+00 ... (remaining 4635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 5874 2.75 - 5.50: 426 5.50 - 8.25: 90 8.25 - 11.00: 5 11.00 - 13.75: 5 Bond angle restraints: 6400 Sorted by residual: angle pdb=" N TYR D 304 " pdb=" CA TYR D 304 " pdb=" C TYR D 304 " ideal model delta sigma weight residual 107.60 121.35 -13.75 1.83e+00 2.99e-01 5.65e+01 angle pdb=" N TYR B 304 " pdb=" CA TYR B 304 " pdb=" C TYR B 304 " ideal model delta sigma weight residual 107.60 121.34 -13.74 1.83e+00 2.99e-01 5.64e+01 angle pdb=" N TYR C 304 " pdb=" CA TYR C 304 " pdb=" C TYR C 304 " ideal model delta sigma weight residual 107.60 121.32 -13.72 1.83e+00 2.99e-01 5.62e+01 angle pdb=" N TYR A 304 " pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 107.60 121.31 -13.71 1.83e+00 2.99e-01 5.62e+01 angle pdb=" N TYR E 304 " pdb=" CA TYR E 304 " pdb=" C TYR E 304 " ideal model delta sigma weight residual 107.60 121.31 -13.71 1.83e+00 2.99e-01 5.61e+01 ... (remaining 6395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 2527 11.99 - 23.97: 123 23.97 - 35.95: 10 35.95 - 47.94: 15 47.94 - 59.92: 5 Dihedral angle restraints: 2680 sinusoidal: 900 harmonic: 1780 Sorted by residual: dihedral pdb=" CA GLY D 317 " pdb=" C GLY D 317 " pdb=" N THR D 318 " pdb=" CA THR D 318 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY B 317 " pdb=" C GLY B 317 " pdb=" N THR B 318 " pdb=" CA THR B 318 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLY E 317 " pdb=" C GLY E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 2677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 702 0.061 - 0.122: 107 0.122 - 0.182: 11 0.182 - 0.243: 0 0.243 - 0.304: 5 Chirality restraints: 825 Sorted by residual: chirality pdb=" CA TYR E 304 " pdb=" N TYR E 304 " pdb=" C TYR E 304 " pdb=" CB TYR E 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA TYR D 304 " pdb=" N TYR D 304 " pdb=" C TYR D 304 " pdb=" CB TYR D 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA TYR C 304 " pdb=" N TYR C 304 " pdb=" C TYR C 304 " pdb=" CB TYR C 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 822 not shown) Planarity restraints: 795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 268 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO D 269 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 268 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO C 269 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 260 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO B 261 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.037 5.00e-02 4.00e+02 ... (remaining 792 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 15 1.82 - 2.59: 135 2.59 - 3.36: 6419 3.36 - 4.13: 10246 4.13 - 4.90: 17972 Nonbonded interactions: 34787 Sorted by model distance: nonbonded pdb=" O ASP A 309 " pdb=" OD2 ASP B 309 " model vdw 1.047 3.040 nonbonded pdb=" O ASP B 309 " pdb=" OD2 ASP D 309 " model vdw 1.047 3.040 nonbonded pdb=" O ASP C 309 " pdb=" OD2 ASP A 309 " model vdw 1.048 3.040 nonbonded pdb=" OD2 ASP C 309 " pdb=" O ASP E 309 " model vdw 1.048 3.040 nonbonded pdb=" O ASP D 309 " pdb=" OD2 ASP E 309 " model vdw 1.048 3.040 ... (remaining 34782 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 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.030 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: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 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 0.041 4640 Z= 0.553 Angle : 1.616 13.750 6400 Z= 1.065 Chirality : 0.052 0.304 825 Planarity : 0.008 0.062 795 Dihedral : 8.570 59.920 1540 Min Nonbonded Distance : 1.047 Molprobity Statistics. All-atom Clashscore : 61.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.66 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.79 (0.37), residues: 180 loop : -1.29 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR B 275 PHE 0.010 0.002 PHE E 307 TRP 0.020 0.002 TRP E 331 Details of bonding type rmsd covalent geometry : bond 0.00863 ( 4640) covalent geometry : angle 1.61586 ( 6400) hydrogen bonds : bond 0.05385 ( 150) hydrogen bonds : angle 10.61830 ( 405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 THR cc_start: 0.7462 (p) cc_final: 0.6955 (p) REVERT: A 277 THR cc_start: 0.7645 (p) cc_final: 0.7384 (p) REVERT: A 341 MET cc_start: 0.7260 (tpp) cc_final: 0.6909 (tpp) REVERT: B 277 THR cc_start: 0.7264 (p) cc_final: 0.6680 (p) REVERT: D 277 THR cc_start: 0.7582 (p) cc_final: 0.7104 (p) REVERT: D 348 LYS cc_start: 0.7769 (mttt) cc_final: 0.7324 (mttt) REVERT: E 348 LYS cc_start: 0.7677 (mttt) cc_final: 0.7329 (mttt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0498 time to fit residues: 16.4174 Evaluate side-chains 170 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 GLN A 305 GLN A 360 GLN B 276 GLN B 305 GLN B 360 GLN D 305 GLN D 360 GLN E 305 GLN E 360 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122078 restraints weight = 8874.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126335 restraints weight = 5329.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129414 restraints weight = 3790.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131565 restraints weight = 3015.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132862 restraints weight = 2593.492| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4640 Z= 0.260 Angle : 0.822 7.355 6400 Z= 0.455 Chirality : 0.051 0.150 825 Planarity : 0.007 0.057 795 Dihedral : 7.925 25.714 640 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.10 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -1.09 (0.34), residues: 245 loop : -1.62 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR D 275 PHE 0.022 0.003 PHE D 307 TRP 0.009 0.002 TRP D 331 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 4640) covalent geometry : angle 0.82225 ( 6400) hydrogen bonds : bond 0.05025 ( 150) hydrogen bonds : angle 8.01729 ( 405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 251 PHE cc_start: 0.6736 (p90) cc_final: 0.6524 (p90) REVERT: C 275 TYR cc_start: 0.8537 (m-80) cc_final: 0.8178 (m-80) REVERT: C 276 GLN cc_start: 0.8375 (tt0) cc_final: 0.7408 (tt0) REVERT: C 284 LEU cc_start: 0.9341 (mt) cc_final: 0.8981 (mt) REVERT: C 311 PHE cc_start: 0.9192 (t80) cc_final: 0.8820 (t80) REVERT: C 318 THR cc_start: 0.8832 (p) cc_final: 0.8574 (p) REVERT: A 275 TYR cc_start: 0.8543 (m-80) cc_final: 0.7435 (m-80) REVERT: A 284 LEU cc_start: 0.9260 (mt) cc_final: 0.8906 (mt) REVERT: A 311 PHE cc_start: 0.9299 (t80) cc_final: 0.8881 (t80) REVERT: B 262 GLN cc_start: 0.8421 (pp30) cc_final: 0.7726 (pp30) REVERT: B 264 LEU cc_start: 0.9046 (pp) cc_final: 0.8701 (mm) REVERT: B 275 TYR cc_start: 0.8462 (m-80) cc_final: 0.8007 (m-80) REVERT: B 276 GLN cc_start: 0.8603 (tt0) cc_final: 0.8194 (tt0) REVERT: B 311 PHE cc_start: 0.9315 (t80) cc_final: 0.8870 (t80) REVERT: B 340 THR cc_start: 0.7584 (p) cc_final: 0.7203 (p) REVERT: D 284 LEU cc_start: 0.9087 (mt) cc_final: 0.8762 (mt) REVERT: D 339 LEU cc_start: 0.8453 (mt) cc_final: 0.8246 (mt) REVERT: D 340 THR cc_start: 0.7602 (p) cc_final: 0.7239 (p) REVERT: E 275 TYR cc_start: 0.8440 (m-80) cc_final: 0.8081 (m-80) REVERT: E 318 THR cc_start: 0.8840 (p) cc_final: 0.8612 (p) REVERT: E 340 THR cc_start: 0.7562 (p) cc_final: 0.7221 (p) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.0510 time to fit residues: 15.5757 Evaluate side-chains 189 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 305 GLN A 276 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.166149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115444 restraints weight = 9224.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119206 restraints weight = 6075.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121588 restraints weight = 4593.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123217 restraints weight = 3845.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123982 restraints weight = 3422.355| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4640 Z= 0.185 Angle : 0.708 6.896 6400 Z= 0.387 Chirality : 0.048 0.166 825 Planarity : 0.006 0.058 795 Dihedral : 6.896 20.005 640 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.98 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.70 (0.37), residues: 245 loop : -1.80 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR D 275 PHE 0.015 0.002 PHE D 311 TRP 0.006 0.001 TRP D 331 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 4640) covalent geometry : angle 0.70797 ( 6400) hydrogen bonds : bond 0.04237 ( 150) hydrogen bonds : angle 7.32061 ( 405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.161 Fit side-chains REVERT: C 275 TYR cc_start: 0.8481 (m-80) cc_final: 0.7799 (m-80) REVERT: C 308 ASP cc_start: 0.9049 (m-30) cc_final: 0.8814 (m-30) REVERT: C 311 PHE cc_start: 0.9277 (t80) cc_final: 0.8894 (t80) REVERT: C 318 THR cc_start: 0.9004 (p) cc_final: 0.8760 (p) REVERT: C 340 THR cc_start: 0.7809 (p) cc_final: 0.7498 (p) REVERT: A 275 TYR cc_start: 0.8292 (m-80) cc_final: 0.7470 (m-80) REVERT: A 308 ASP cc_start: 0.9155 (m-30) cc_final: 0.8952 (m-30) REVERT: A 311 PHE cc_start: 0.9295 (t80) cc_final: 0.8980 (t80) REVERT: A 318 THR cc_start: 0.8977 (p) cc_final: 0.8764 (p) REVERT: A 339 LEU cc_start: 0.8452 (mt) cc_final: 0.8089 (mt) REVERT: B 308 ASP cc_start: 0.8926 (m-30) cc_final: 0.8683 (m-30) REVERT: B 311 PHE cc_start: 0.9215 (t80) cc_final: 0.8952 (t80) REVERT: B 339 LEU cc_start: 0.8503 (mt) cc_final: 0.8151 (mt) REVERT: B 340 THR cc_start: 0.7988 (p) cc_final: 0.7643 (p) REVERT: D 329 VAL cc_start: 0.9539 (t) cc_final: 0.9222 (t) REVERT: D 340 THR cc_start: 0.7853 (p) cc_final: 0.7543 (p) REVERT: E 308 ASP cc_start: 0.9111 (m-30) cc_final: 0.8774 (m-30) REVERT: E 318 THR cc_start: 0.8914 (p) cc_final: 0.8631 (p) REVERT: E 339 LEU cc_start: 0.8444 (mt) cc_final: 0.8205 (mt) REVERT: E 340 THR cc_start: 0.7948 (p) cc_final: 0.7320 (t) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.0491 time to fit residues: 15.1784 Evaluate side-chains 195 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 30 optimal weight: 5.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** 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 = 0.4058 r_free = 0.4058 target = 0.169892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116924 restraints weight = 8771.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120806 restraints weight = 5608.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123452 restraints weight = 4205.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125193 restraints weight = 3484.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126068 restraints weight = 3087.738| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4640 Z= 0.202 Angle : 0.685 6.153 6400 Z= 0.379 Chirality : 0.048 0.154 825 Planarity : 0.007 0.068 795 Dihedral : 6.743 21.797 640 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.91 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.66 (0.36), residues: 245 loop : -1.75 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR E 275 PHE 0.021 0.002 PHE B 297 TRP 0.005 0.001 TRP C 331 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 4640) covalent geometry : angle 0.68535 ( 6400) hydrogen bonds : bond 0.04543 ( 150) hydrogen bonds : angle 7.28039 ( 405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.138 Fit side-chains REVERT: C 275 TYR cc_start: 0.8384 (m-80) cc_final: 0.7995 (m-80) REVERT: C 311 PHE cc_start: 0.9228 (t80) cc_final: 0.8829 (t80) REVERT: C 340 THR cc_start: 0.7805 (p) cc_final: 0.7448 (p) REVERT: A 264 LEU cc_start: 0.8967 (mm) cc_final: 0.8706 (mm) REVERT: A 275 TYR cc_start: 0.8257 (m-80) cc_final: 0.7673 (m-80) REVERT: A 311 PHE cc_start: 0.9389 (t80) cc_final: 0.9087 (t80) REVERT: A 339 LEU cc_start: 0.8558 (mt) cc_final: 0.8356 (mt) REVERT: B 275 TYR cc_start: 0.8184 (m-80) cc_final: 0.7615 (m-80) REVERT: B 308 ASP cc_start: 0.9021 (m-30) cc_final: 0.8755 (m-30) REVERT: B 311 PHE cc_start: 0.9263 (t80) cc_final: 0.8983 (t80) REVERT: B 340 THR cc_start: 0.7988 (p) cc_final: 0.7603 (p) REVERT: D 340 THR cc_start: 0.7796 (p) cc_final: 0.7459 (p) REVERT: E 264 LEU cc_start: 0.8869 (mm) cc_final: 0.8568 (mm) REVERT: E 275 TYR cc_start: 0.8440 (m-80) cc_final: 0.7905 (m-80) REVERT: E 308 ASP cc_start: 0.9062 (m-30) cc_final: 0.8770 (m-30) REVERT: E 318 THR cc_start: 0.8935 (p) cc_final: 0.8669 (p) REVERT: E 339 LEU cc_start: 0.8531 (mt) cc_final: 0.8263 (mt) REVERT: E 340 THR cc_start: 0.7824 (p) cc_final: 0.7159 (t) REVERT: E 348 LYS cc_start: 0.9369 (mtmm) cc_final: 0.8733 (mtmm) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0478 time to fit residues: 14.7970 Evaluate side-chains 201 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.0170 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.0570 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 0.0030 overall best weight: 0.9348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN D 253 ASN D 282 GLN E 256 ASN E 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121753 restraints weight = 8784.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125718 restraints weight = 5610.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128161 restraints weight = 4185.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130466 restraints weight = 3505.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131600 restraints weight = 3066.205| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4640 Z= 0.129 Angle : 0.667 7.623 6400 Z= 0.359 Chirality : 0.050 0.158 825 Planarity : 0.006 0.065 795 Dihedral : 6.270 20.121 640 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.19 % Allowed : 2.50 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.87 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.58 (0.34), residues: 245 loop : -1.76 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR B 304 PHE 0.021 0.002 PHE B 297 TRP 0.008 0.001 TRP A 331 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4640) covalent geometry : angle 0.66663 ( 6400) hydrogen bonds : bond 0.03930 ( 150) hydrogen bonds : angle 7.01042 ( 405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: C 311 PHE cc_start: 0.9185 (t80) cc_final: 0.8743 (t80) REVERT: C 314 PHE cc_start: 0.7945 (m-80) cc_final: 0.7611 (m-10) REVERT: C 340 THR cc_start: 0.7827 (p) cc_final: 0.7475 (p) REVERT: A 251 PHE cc_start: 0.6558 (p90) cc_final: 0.6157 (p90) REVERT: A 266 MET cc_start: 0.5764 (mpp) cc_final: 0.5322 (mpp) REVERT: A 275 TYR cc_start: 0.8346 (m-80) cc_final: 0.7861 (m-80) REVERT: A 311 PHE cc_start: 0.9313 (t80) cc_final: 0.8968 (t80) REVERT: A 340 THR cc_start: 0.7738 (p) cc_final: 0.7278 (p) REVERT: A 348 LYS cc_start: 0.9338 (mtmm) cc_final: 0.8995 (mtmm) REVERT: B 264 LEU cc_start: 0.8851 (mm) cc_final: 0.8601 (mm) REVERT: B 275 TYR cc_start: 0.8278 (m-80) cc_final: 0.7806 (m-80) REVERT: B 308 ASP cc_start: 0.8944 (m-30) cc_final: 0.8697 (m-30) REVERT: B 311 PHE cc_start: 0.9226 (t80) cc_final: 0.8849 (t80) REVERT: B 340 THR cc_start: 0.8032 (p) cc_final: 0.7657 (p) REVERT: D 314 PHE cc_start: 0.8195 (m-80) cc_final: 0.7844 (m-80) REVERT: D 340 THR cc_start: 0.7807 (p) cc_final: 0.7421 (p) REVERT: E 275 TYR cc_start: 0.8372 (m-80) cc_final: 0.7884 (m-80) REVERT: E 308 ASP cc_start: 0.9018 (m-30) cc_final: 0.8712 (m-30) REVERT: E 340 THR cc_start: 0.7853 (p) cc_final: 0.7197 (t) outliers start: 1 outliers final: 1 residues processed: 230 average time/residue: 0.0480 time to fit residues: 15.1719 Evaluate side-chains 214 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 ASN ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.173376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118943 restraints weight = 8731.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123008 restraints weight = 5519.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125571 restraints weight = 4145.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127436 restraints weight = 3456.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128385 restraints weight = 3057.101| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4640 Z= 0.199 Angle : 0.682 5.998 6400 Z= 0.371 Chirality : 0.049 0.145 825 Planarity : 0.006 0.065 795 Dihedral : 6.398 21.638 640 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.85 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.51 (0.33), residues: 245 loop : -1.79 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR C 275 PHE 0.021 0.002 PHE E 311 TRP 0.005 0.001 TRP E 331 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 4640) covalent geometry : angle 0.68171 ( 6400) hydrogen bonds : bond 0.04566 ( 150) hydrogen bonds : angle 7.22286 ( 405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8841 (m-10) cc_final: 0.8286 (m-80) REVERT: C 311 PHE cc_start: 0.9191 (t80) cc_final: 0.8699 (t80) REVERT: C 340 THR cc_start: 0.7817 (p) cc_final: 0.7442 (p) REVERT: A 251 PHE cc_start: 0.6681 (p90) cc_final: 0.6287 (p90) REVERT: A 266 MET cc_start: 0.6002 (mpp) cc_final: 0.5700 (mpp) REVERT: A 275 TYR cc_start: 0.8400 (m-80) cc_final: 0.7963 (m-80) REVERT: A 311 PHE cc_start: 0.9378 (t80) cc_final: 0.9040 (t80) REVERT: A 340 THR cc_start: 0.7723 (p) cc_final: 0.7292 (p) REVERT: A 348 LYS cc_start: 0.9392 (mtmm) cc_final: 0.9007 (mtmm) REVERT: B 275 TYR cc_start: 0.8386 (m-80) cc_final: 0.8042 (m-80) REVERT: B 308 ASP cc_start: 0.8963 (m-30) cc_final: 0.8747 (m-30) REVERT: B 311 PHE cc_start: 0.9303 (t80) cc_final: 0.8913 (t80) REVERT: B 340 THR cc_start: 0.8043 (p) cc_final: 0.7640 (p) REVERT: B 348 LYS cc_start: 0.9512 (mtmm) cc_final: 0.9219 (mtmm) REVERT: D 251 PHE cc_start: 0.6583 (p90) cc_final: 0.6099 (p90) REVERT: D 340 THR cc_start: 0.7894 (p) cc_final: 0.7518 (p) REVERT: E 308 ASP cc_start: 0.8950 (m-30) cc_final: 0.8671 (m-30) REVERT: E 340 THR cc_start: 0.8300 (p) cc_final: 0.7684 (t) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.0461 time to fit residues: 14.2736 Evaluate side-chains 204 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 0.0060 chunk 44 optimal weight: 4.9990 chunk 50 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.176863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122480 restraints weight = 8739.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126504 restraints weight = 5540.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129459 restraints weight = 4153.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131184 restraints weight = 3437.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.132579 restraints weight = 3052.787| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4640 Z= 0.131 Angle : 0.657 7.803 6400 Z= 0.350 Chirality : 0.050 0.170 825 Planarity : 0.006 0.062 795 Dihedral : 6.155 20.577 640 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.19 % Allowed : 1.54 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.71 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.38 (0.33), residues: 245 loop : -1.72 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR C 275 PHE 0.040 0.002 PHE B 314 TRP 0.003 0.001 TRP A 331 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4640) covalent geometry : angle 0.65660 ( 6400) hydrogen bonds : bond 0.04076 ( 150) hydrogen bonds : angle 7.03693 ( 405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.162 Fit side-chains REVERT: C 275 TYR cc_start: 0.8886 (m-10) cc_final: 0.8664 (m-10) REVERT: C 311 PHE cc_start: 0.9213 (t80) cc_final: 0.8702 (t80) REVERT: C 340 THR cc_start: 0.7766 (p) cc_final: 0.7400 (p) REVERT: A 251 PHE cc_start: 0.6443 (p90) cc_final: 0.6027 (p90) REVERT: A 266 MET cc_start: 0.5817 (mpp) cc_final: 0.5607 (mpp) REVERT: A 275 TYR cc_start: 0.8396 (m-80) cc_final: 0.8012 (m-80) REVERT: A 311 PHE cc_start: 0.9363 (t80) cc_final: 0.9028 (t80) REVERT: A 340 THR cc_start: 0.7592 (p) cc_final: 0.7173 (p) REVERT: B 311 PHE cc_start: 0.9288 (t80) cc_final: 0.8961 (t80) REVERT: B 314 PHE cc_start: 0.7465 (m-10) cc_final: 0.7257 (m-10) REVERT: B 340 THR cc_start: 0.8443 (p) cc_final: 0.8143 (p) REVERT: B 348 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9128 (mtmm) REVERT: D 314 PHE cc_start: 0.8196 (m-80) cc_final: 0.7851 (m-80) REVERT: D 340 THR cc_start: 0.7784 (p) cc_final: 0.7389 (p) REVERT: E 308 ASP cc_start: 0.8899 (m-30) cc_final: 0.8650 (m-30) REVERT: E 340 THR cc_start: 0.8163 (p) cc_final: 0.7581 (t) REVERT: E 348 LYS cc_start: 0.9328 (mtmm) cc_final: 0.8923 (mtmm) outliers start: 1 outliers final: 1 residues processed: 221 average time/residue: 0.0441 time to fit residues: 13.5026 Evaluate side-chains 207 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.171882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117169 restraints weight = 8920.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121116 restraints weight = 5643.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123980 restraints weight = 4223.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125714 restraints weight = 3501.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127109 restraints weight = 3101.104| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 4640 Z= 0.231 Angle : 0.690 6.142 6400 Z= 0.376 Chirality : 0.050 0.212 825 Planarity : 0.006 0.070 795 Dihedral : 6.443 21.855 640 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.79 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.38 (0.33), residues: 245 loop : -1.83 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR E 275 PHE 0.029 0.002 PHE B 314 TRP 0.008 0.001 TRP E 331 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 4640) covalent geometry : angle 0.68961 ( 6400) hydrogen bonds : bond 0.04906 ( 150) hydrogen bonds : angle 7.14331 ( 405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.145 Fit side-chains REVERT: C 264 LEU cc_start: 0.9009 (mm) cc_final: 0.8593 (mm) REVERT: C 340 THR cc_start: 0.7817 (p) cc_final: 0.7386 (p) REVERT: A 251 PHE cc_start: 0.6524 (p90) cc_final: 0.6186 (p90) REVERT: A 275 TYR cc_start: 0.8460 (m-80) cc_final: 0.8102 (m-80) REVERT: A 311 PHE cc_start: 0.9389 (t80) cc_final: 0.8997 (t80) REVERT: A 339 LEU cc_start: 0.8827 (mt) cc_final: 0.8434 (mt) REVERT: A 340 THR cc_start: 0.7660 (p) cc_final: 0.7209 (p) REVERT: A 348 LYS cc_start: 0.9429 (mtmm) cc_final: 0.9188 (mtmm) REVERT: B 311 PHE cc_start: 0.9374 (t80) cc_final: 0.9010 (t80) REVERT: B 314 PHE cc_start: 0.7671 (m-10) cc_final: 0.7467 (m-10) REVERT: B 339 LEU cc_start: 0.8476 (mt) cc_final: 0.8219 (mt) REVERT: B 340 THR cc_start: 0.8453 (p) cc_final: 0.8108 (p) REVERT: B 348 LYS cc_start: 0.9497 (mtmm) cc_final: 0.9090 (mtmm) REVERT: D 275 TYR cc_start: 0.8832 (m-80) cc_final: 0.8428 (m-10) REVERT: D 340 THR cc_start: 0.8216 (p) cc_final: 0.7878 (p) REVERT: E 308 ASP cc_start: 0.8905 (m-30) cc_final: 0.8703 (m-30) REVERT: E 340 THR cc_start: 0.8216 (p) cc_final: 0.7858 (p) REVERT: E 348 LYS cc_start: 0.9374 (mtmm) cc_final: 0.9017 (mtmm) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.0485 time to fit residues: 14.4325 Evaluate side-chains 181 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.0670 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 overall best weight: 2.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN D 282 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.175055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119280 restraints weight = 8800.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123130 restraints weight = 5714.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125845 restraints weight = 4354.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127786 restraints weight = 3654.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128678 restraints weight = 3262.010| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4640 Z= 0.167 Angle : 0.687 7.959 6400 Z= 0.369 Chirality : 0.052 0.193 825 Planarity : 0.006 0.063 795 Dihedral : 6.454 21.584 640 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.63 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.25 (0.33), residues: 245 loop : -1.73 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR B 275 PHE 0.021 0.002 PHE B 314 TRP 0.011 0.001 TRP E 331 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 4640) covalent geometry : angle 0.68710 ( 6400) hydrogen bonds : bond 0.04522 ( 150) hydrogen bonds : angle 7.05373 ( 405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: C 340 THR cc_start: 0.7808 (p) cc_final: 0.7419 (p) REVERT: A 275 TYR cc_start: 0.8456 (m-80) cc_final: 0.8131 (m-80) REVERT: A 308 ASP cc_start: 0.8940 (m-30) cc_final: 0.8717 (m-30) REVERT: A 311 PHE cc_start: 0.9381 (t80) cc_final: 0.8960 (t80) REVERT: A 340 THR cc_start: 0.7709 (p) cc_final: 0.7312 (p) REVERT: A 348 LYS cc_start: 0.9423 (mtmm) cc_final: 0.9202 (mtmm) REVERT: B 311 PHE cc_start: 0.9337 (t80) cc_final: 0.8965 (t80) REVERT: B 339 LEU cc_start: 0.8430 (mt) cc_final: 0.8223 (mt) REVERT: B 340 THR cc_start: 0.8378 (p) cc_final: 0.8040 (p) REVERT: B 348 LYS cc_start: 0.9468 (mtmm) cc_final: 0.9224 (mtmm) REVERT: D 251 PHE cc_start: 0.6417 (p90) cc_final: 0.6135 (p90) REVERT: D 264 LEU cc_start: 0.8908 (mm) cc_final: 0.8423 (mm) REVERT: D 275 TYR cc_start: 0.8851 (m-80) cc_final: 0.8424 (m-10) REVERT: D 314 PHE cc_start: 0.8270 (m-80) cc_final: 0.7969 (m-80) REVERT: D 340 THR cc_start: 0.8175 (p) cc_final: 0.7837 (p) REVERT: E 275 TYR cc_start: 0.8713 (m-80) cc_final: 0.8468 (m-80) REVERT: E 308 ASP cc_start: 0.8819 (m-30) cc_final: 0.8599 (m-30) REVERT: E 340 THR cc_start: 0.8079 (p) cc_final: 0.7749 (p) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0462 time to fit residues: 13.2104 Evaluate side-chains 190 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114459 restraints weight = 8920.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118374 restraints weight = 5868.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120819 restraints weight = 4426.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122607 restraints weight = 3732.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124110 restraints weight = 3277.678| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 4640 Z= 0.249 Angle : 0.741 6.330 6400 Z= 0.404 Chirality : 0.052 0.222 825 Planarity : 0.006 0.068 795 Dihedral : 6.634 23.123 640 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.77 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.28 (0.33), residues: 245 loop : -1.88 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.001 TYR B 275 PHE 0.041 0.002 PHE E 311 TRP 0.021 0.002 TRP A 331 Details of bonding type rmsd covalent geometry : bond 0.00587 ( 4640) covalent geometry : angle 0.74100 ( 6400) hydrogen bonds : bond 0.05328 ( 150) hydrogen bonds : angle 7.08811 ( 405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.199 Fit side-chains REVERT: C 275 TYR cc_start: 0.8780 (m-10) cc_final: 0.8490 (m-10) REVERT: C 282 GLN cc_start: 0.6867 (pt0) cc_final: 0.6577 (pt0) REVERT: C 340 THR cc_start: 0.7780 (p) cc_final: 0.7375 (p) REVERT: A 275 TYR cc_start: 0.8458 (m-80) cc_final: 0.8096 (m-80) REVERT: A 308 ASP cc_start: 0.8961 (m-30) cc_final: 0.8756 (m-30) REVERT: A 311 PHE cc_start: 0.9427 (t80) cc_final: 0.8985 (t80) REVERT: B 275 TYR cc_start: 0.8352 (m-80) cc_final: 0.7481 (m-80) REVERT: B 340 THR cc_start: 0.8324 (p) cc_final: 0.7964 (p) REVERT: B 348 LYS cc_start: 0.9521 (mtmm) cc_final: 0.9256 (mtmm) REVERT: D 251 PHE cc_start: 0.6440 (p90) cc_final: 0.6146 (p90) REVERT: D 275 TYR cc_start: 0.8888 (m-80) cc_final: 0.8456 (m-10) REVERT: D 311 PHE cc_start: 0.9369 (t80) cc_final: 0.9001 (t80) REVERT: D 340 THR cc_start: 0.8253 (p) cc_final: 0.7973 (p) REVERT: E 275 TYR cc_start: 0.8793 (m-80) cc_final: 0.8209 (m-80) REVERT: E 311 PHE cc_start: 0.9040 (t80) cc_final: 0.8683 (t80) REVERT: E 339 LEU cc_start: 0.8654 (mt) cc_final: 0.8360 (mt) REVERT: E 340 THR cc_start: 0.8202 (p) cc_final: 0.7829 (p) REVERT: E 348 LYS cc_start: 0.9385 (mtmm) cc_final: 0.9008 (mtmm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0507 time to fit residues: 13.6218 Evaluate side-chains 180 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.171486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120307 restraints weight = 8655.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124362 restraints weight = 5316.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127175 restraints weight = 3887.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128978 restraints weight = 3154.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.129617 restraints weight = 2754.724| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4640 Z= 0.213 Angle : 0.719 7.616 6400 Z= 0.392 Chirality : 0.052 0.275 825 Planarity : 0.006 0.063 795 Dihedral : 6.644 24.974 640 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.84 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.36 (0.33), residues: 245 loop : -1.91 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR B 304 PHE 0.027 0.002 PHE B 311 TRP 0.019 0.002 TRP A 331 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 4640) covalent geometry : angle 0.71889 ( 6400) hydrogen bonds : bond 0.05098 ( 150) hydrogen bonds : angle 6.95818 ( 405) =============================================================================== Job complete usr+sys time: 927.43 seconds wall clock time: 16 minutes 39.47 seconds (999.47 seconds total)