Starting phenix.real_space_refine on Tue Mar 3 11:03:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n37_9339/03_2026/6n37_9339.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n37_9339/03_2026/6n37_9339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n37_9339/03_2026/6n37_9339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n37_9339/03_2026/6n37_9339.map" model { file = "/net/cci-nas-00/data/ceres_data/6n37_9339/03_2026/6n37_9339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n37_9339/03_2026/6n37_9339.cif" } resolution = 3.8 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 50 5.16 5 C 1590 2.51 5 N 450 2.21 5 O 490 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: 2580 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.21, per 1000 atoms: 0.08 Number of scatterers: 2580 At special positions: 0 Unit cell: (86.184, 54.264, 45.752, 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 50 16.00 O 490 8.00 N 450 7.00 C 1590 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: 0.15 Conformation dependent library (CDL) restraints added in 99.8 milliseconds 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 323 through 324 removed outlier: 6.928A pdb=" N MET A 323 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET E 323 " --> pdb=" O ALA I 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 335 through 342 removed outlier: 5.803A pdb=" N GLY D 335 " --> pdb=" O MET H 336 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLY H 338 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET D 337 " --> pdb=" O GLY H 338 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU H 340 " --> pdb=" O MET D 337 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N MET D 339 " --> pdb=" O LEU H 340 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N SER H 342 " --> pdb=" O MET D 339 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA D 341 " --> pdb=" O SER H 342 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET D 337 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A 338 " --> pdb=" O MET D 337 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N MET D 339 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 340 " --> pdb=" O MET D 339 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA D 341 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER A 342 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY E 335 " --> pdb=" O TRP A 334 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET A 336 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET E 336 " --> pdb=" O GLY I 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 345 through 346 removed outlier: 6.700A pdb=" N ASN D 345 " --> pdb=" O GLN H 346 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLN D 346 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 345 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY E 335 " --> pdb=" O TRP A 334 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET A 336 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASN I 345 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN E 344 " --> pdb=" O ASN I 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 323 through 324 removed outlier: 6.966A pdb=" N MET C 323 " --> pdb=" O ALA G 324 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET B 323 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 335 through 342 removed outlier: 6.770A pdb=" N MET C 336 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET B 336 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY B 335 " --> pdb=" O MET F 336 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLY F 338 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N MET B 337 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU F 340 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N MET B 339 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N SER F 342 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 341 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLY F 335 " --> pdb=" O MET J 336 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N GLY J 338 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET F 337 " --> pdb=" O GLY J 338 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU J 340 " --> pdb=" O MET F 337 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET F 339 " --> pdb=" O LEU J 340 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N SER J 342 " --> pdb=" O MET F 339 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA F 341 " --> pdb=" O SER J 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 345 through 346 removed outlier: 6.607A pdb=" N ASN B 345 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN F 345 " --> pdb=" O GLN J 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 323 through 324 45 hydrogen bonds defined for protein. 135 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: 0.24 Time building geometry restraints manager: 0.23 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: 860 1.34 - 1.45: 450 1.45 - 1.57: 1210 1.57 - 1.69: 0 1.69 - 1.80: 100 Bond restraints: 2620 Sorted by residual: bond pdb=" CB MET H 322 " pdb=" CG MET H 322 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" CB MET F 322 " pdb=" CG MET F 322 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CB MET E 322 " pdb=" CG MET E 322 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CB MET B 322 " pdb=" CG MET B 322 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" CB MET A 322 " pdb=" CG MET A 322 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 ... (remaining 2615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 3013 1.61 - 3.22: 337 3.22 - 4.83: 100 4.83 - 6.43: 30 6.43 - 8.04: 30 Bond angle restraints: 3510 Sorted by residual: angle pdb=" C GLY B 314 " pdb=" N ALA B 315 " pdb=" CA ALA B 315 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C GLY I 314 " pdb=" N ALA I 315 " pdb=" CA ALA I 315 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C GLY G 314 " pdb=" N ALA G 315 " pdb=" CA ALA G 315 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C GLY D 314 " pdb=" N ALA D 315 " pdb=" CA ALA D 315 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C GLY C 314 " pdb=" N ALA C 315 " pdb=" CA ALA C 315 " ideal model delta sigma weight residual 121.54 129.55 -8.01 1.91e+00 2.74e-01 1.76e+01 ... (remaining 3505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.11: 1330 13.11 - 26.23: 180 26.23 - 39.34: 20 39.34 - 52.45: 10 52.45 - 65.56: 30 Dihedral angle restraints: 1570 sinusoidal: 560 harmonic: 1010 Sorted by residual: dihedral pdb=" CA GLY D 314 " pdb=" C GLY D 314 " pdb=" N ALA D 315 " pdb=" CA ALA D 315 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY E 314 " pdb=" C GLY E 314 " pdb=" N ALA E 315 " pdb=" CA ALA E 315 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY F 314 " pdb=" C GLY F 314 " pdb=" N ALA F 315 " pdb=" CA ALA F 315 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 1567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 186 0.033 - 0.066: 64 0.066 - 0.099: 70 0.099 - 0.132: 14 0.132 - 0.165: 26 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA PHE C 316 " pdb=" N PHE C 316 " pdb=" C PHE C 316 " pdb=" CB PHE C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA PHE J 316 " pdb=" N PHE J 316 " pdb=" C PHE J 316 " pdb=" CB PHE J 316 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA PHE D 316 " pdb=" N PHE D 316 " pdb=" C PHE D 316 " pdb=" CB PHE D 316 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 357 not shown) Planarity restraints: 470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY J 314 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLY J 314 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY J 314 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA J 315 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 314 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLY B 314 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY B 314 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA B 315 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 314 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.46e+01 pdb=" C GLY H 314 " 0.066 2.00e-02 2.50e+03 pdb=" O GLY H 314 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA H 315 " -0.022 2.00e-02 2.50e+03 ... (remaining 467 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1018 2.90 - 3.40: 2308 3.40 - 3.90: 4160 3.90 - 4.40: 4564 4.40 - 4.90: 9139 Nonbonded interactions: 21189 Sorted by model distance: nonbonded pdb=" N ASN J 319 " pdb=" OD1 ASN J 319 " model vdw 2.399 3.120 nonbonded pdb=" N ASN H 319 " pdb=" OD1 ASN H 319 " model vdw 2.399 3.120 nonbonded pdb=" N ASN G 319 " pdb=" OD1 ASN G 319 " model vdw 2.399 3.120 nonbonded pdb=" N ASN B 319 " pdb=" OD1 ASN B 319 " model vdw 2.400 3.120 nonbonded pdb=" N ASN E 319 " pdb=" OD1 ASN E 319 " model vdw 2.400 3.120 ... (remaining 21184 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.090 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.020 Find NCS groups from input model: 0.020 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 4.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 0.046 2620 Z= 0.405 Angle : 1.419 8.042 3510 Z= 0.765 Chirality : 0.064 0.165 360 Planarity : 0.008 0.038 470 Dihedral : 16.984 65.562 910 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % 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 are not related in a simple way. whole: -5.92 (0.19), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.14), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.008 PHE C 316 TRP 0.006 0.002 TRP C 334 Details of bonding type rmsd covalent geometry : bond 0.00867 ( 2620) covalent geometry : angle 1.41889 ( 3510) hydrogen bonds : bond 0.25003 ( 35) hydrogen bonds : angle 10.72751 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.071 Fit side-chains REVERT: I 336 MET cc_start: 0.8277 (mtm) cc_final: 0.8037 (mtp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0329 time to fit residues: 3.5320 Evaluate side-chains 63 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN B 345 ASN C 345 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN E 345 ASN F 345 ASN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 ASN J 331 GLN J 345 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.148465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.119610 restraints weight = 6226.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.122223 restraints weight = 4043.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.123937 restraints weight = 2927.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.125260 restraints weight = 2319.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.126180 restraints weight = 1921.700| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2620 Z= 0.242 Angle : 0.784 6.146 3510 Z= 0.407 Chirality : 0.039 0.141 360 Planarity : 0.005 0.036 470 Dihedral : 6.949 18.998 350 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.00 % Allowed : 17.60 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.30 (0.20), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.004 PHE E 316 TRP 0.016 0.003 TRP B 334 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 2620) covalent geometry : angle 0.78408 ( 3510) hydrogen bonds : bond 0.03537 ( 35) hydrogen bonds : angle 8.09974 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.067 Fit side-chains REVERT: B 343 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7938 (tp-100) REVERT: F 340 LEU cc_start: 0.9203 (pt) cc_final: 0.8945 (pp) REVERT: I 336 MET cc_start: 0.7795 (mtm) cc_final: 0.7432 (mtp) REVERT: I 343 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7178 (mt0) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.0409 time to fit residues: 3.5757 Evaluate side-chains 71 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain I residue 343 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 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 = 0.4163 r_free = 0.4163 target = 0.142162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.118485 restraints weight = 6150.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.121344 restraints weight = 3804.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.123319 restraints weight = 2737.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.124790 restraints weight = 2131.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.125239 restraints weight = 1741.692| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2620 Z= 0.174 Angle : 0.683 6.612 3510 Z= 0.349 Chirality : 0.036 0.136 360 Planarity : 0.005 0.037 470 Dihedral : 6.106 16.748 350 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.60 % Allowed : 22.80 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.17 (0.20), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE A 316 TRP 0.010 0.002 TRP B 334 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2620) covalent geometry : angle 0.68306 ( 3510) hydrogen bonds : bond 0.03016 ( 35) hydrogen bonds : angle 7.39063 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.070 Fit side-chains REVERT: B 322 MET cc_start: 0.7710 (mtt) cc_final: 0.7444 (mtp) REVERT: H 322 MET cc_start: 0.7482 (mtt) cc_final: 0.6877 (mtt) REVERT: I 336 MET cc_start: 0.7337 (mtm) cc_final: 0.6891 (mtp) REVERT: I 343 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6987 (mt0) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.0334 time to fit residues: 2.8880 Evaluate side-chains 73 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain I residue 343 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 40.0000 chunk 26 optimal weight: 8.9990 chunk 9 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 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 = 0.4165 r_free = 0.4165 target = 0.142505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.118433 restraints weight = 6213.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.121229 restraints weight = 3875.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.123235 restraints weight = 2812.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.124675 restraints weight = 2184.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.125647 restraints weight = 1798.610| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2620 Z= 0.168 Angle : 0.676 6.734 3510 Z= 0.339 Chirality : 0.036 0.135 360 Planarity : 0.005 0.035 470 Dihedral : 5.782 15.371 350 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.40 % Allowed : 24.00 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.13 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE C 316 TRP 0.008 0.002 TRP I 334 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 2620) covalent geometry : angle 0.67604 ( 3510) hydrogen bonds : bond 0.02631 ( 35) hydrogen bonds : angle 7.16684 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.095 Fit side-chains REVERT: F 340 LEU cc_start: 0.9066 (pt) cc_final: 0.8712 (pp) REVERT: H 322 MET cc_start: 0.7582 (mtt) cc_final: 0.7243 (mtt) REVERT: I 336 MET cc_start: 0.7157 (mtm) cc_final: 0.6806 (mtm) REVERT: I 343 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6964 (mt0) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.0400 time to fit residues: 3.4691 Evaluate side-chains 74 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain I residue 343 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 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 = 0.4194 r_free = 0.4194 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.120825 restraints weight = 6138.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.123577 restraints weight = 3811.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.125517 restraints weight = 2755.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.126475 restraints weight = 2165.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.127709 restraints weight = 1886.604| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2620 Z= 0.139 Angle : 0.626 7.004 3510 Z= 0.315 Chirality : 0.035 0.134 360 Planarity : 0.005 0.034 470 Dihedral : 5.435 13.886 350 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.00 % Allowed : 25.20 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.06 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 316 TRP 0.009 0.002 TRP G 334 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2620) covalent geometry : angle 0.62615 ( 3510) hydrogen bonds : bond 0.02437 ( 35) hydrogen bonds : angle 6.95208 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.091 Fit side-chains REVERT: F 340 LEU cc_start: 0.9002 (pt) cc_final: 0.8689 (pp) REVERT: H 322 MET cc_start: 0.7545 (mtt) cc_final: 0.7197 (mtt) REVERT: I 323 MET cc_start: 0.6834 (tpp) cc_final: 0.5458 (pmm) REVERT: I 343 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.6843 (mt0) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 0.0390 time to fit residues: 3.3620 Evaluate side-chains 69 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain J residue 322 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 30.0000 chunk 16 optimal weight: 40.0000 chunk 22 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 40.0000 chunk 18 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.143557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.119480 restraints weight = 6150.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.122217 restraints weight = 3849.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.124128 restraints weight = 2784.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.125547 restraints weight = 2189.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.126242 restraints weight = 1801.429| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2620 Z= 0.146 Angle : 0.642 6.834 3510 Z= 0.320 Chirality : 0.035 0.133 360 Planarity : 0.004 0.032 470 Dihedral : 5.341 13.582 350 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.60 % Allowed : 25.60 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE A 316 TRP 0.007 0.001 TRP B 334 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 2620) covalent geometry : angle 0.64240 ( 3510) hydrogen bonds : bond 0.02634 ( 35) hydrogen bonds : angle 6.89424 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.096 Fit side-chains REVERT: F 340 LEU cc_start: 0.9055 (pt) cc_final: 0.8765 (pp) REVERT: H 322 MET cc_start: 0.7633 (mtt) cc_final: 0.7396 (mtt) REVERT: I 323 MET cc_start: 0.6832 (tpp) cc_final: 0.5453 (pmm) REVERT: I 343 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6829 (mt0) outliers start: 9 outliers final: 6 residues processed: 65 average time/residue: 0.0398 time to fit residues: 3.3572 Evaluate side-chains 71 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain I residue 319 ASN Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain J residue 322 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 22 optimal weight: 40.0000 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 ASN H 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.142735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.118358 restraints weight = 6118.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.121068 restraints weight = 3895.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.122972 restraints weight = 2825.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.124226 restraints weight = 2217.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.125293 restraints weight = 1860.780| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2620 Z= 0.159 Angle : 0.657 7.132 3510 Z= 0.327 Chirality : 0.035 0.133 360 Planarity : 0.004 0.030 470 Dihedral : 5.399 14.238 350 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 5.20 % Allowed : 24.80 % Favored : 70.00 % 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 are not related in a simple way. whole: -5.06 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.18), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE A 316 TRP 0.006 0.001 TRP I 334 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2620) covalent geometry : angle 0.65700 ( 3510) hydrogen bonds : bond 0.02712 ( 35) hydrogen bonds : angle 6.91323 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.098 Fit side-chains REVERT: A 323 MET cc_start: 0.7531 (tpt) cc_final: 0.7330 (tpt) REVERT: D 337 MET cc_start: 0.8101 (ptp) cc_final: 0.7675 (ptp) REVERT: E 323 MET cc_start: 0.7406 (tmm) cc_final: 0.6912 (tmm) REVERT: F 340 LEU cc_start: 0.9045 (pt) cc_final: 0.8766 (pp) REVERT: I 343 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6857 (mt0) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 0.0408 time to fit residues: 3.5538 Evaluate side-chains 74 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 343 GLN Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain J residue 322 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 40.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 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 = 0.4182 r_free = 0.4182 target = 0.143655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.119137 restraints weight = 6232.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.121899 restraints weight = 3933.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.123863 restraints weight = 2846.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.124973 restraints weight = 2225.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.126173 restraints weight = 1899.225| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2620 Z= 0.147 Angle : 0.667 9.040 3510 Z= 0.326 Chirality : 0.035 0.133 360 Planarity : 0.004 0.031 470 Dihedral : 5.248 15.206 350 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 4.40 % Allowed : 25.20 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.01 (0.24), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.18), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 316 TRP 0.007 0.001 TRP I 334 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2620) covalent geometry : angle 0.66674 ( 3510) hydrogen bonds : bond 0.02734 ( 35) hydrogen bonds : angle 6.88256 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.093 Fit side-chains REVERT: B 323 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6953 (tpp) REVERT: E 323 MET cc_start: 0.7432 (tmm) cc_final: 0.6996 (tmm) REVERT: I 343 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6875 (mt0) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.0424 time to fit residues: 3.6386 Evaluate side-chains 72 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain J residue 322 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.144865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.120562 restraints weight = 6192.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.123349 restraints weight = 3913.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.125314 restraints weight = 2833.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.126743 restraints weight = 2212.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.127836 restraints weight = 1825.192| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2620 Z= 0.137 Angle : 0.675 8.474 3510 Z= 0.324 Chirality : 0.035 0.131 360 Planarity : 0.004 0.030 470 Dihedral : 5.125 14.487 350 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.80 % Allowed : 26.40 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.93 (0.24), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.19), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 316 TRP 0.007 0.001 TRP D 334 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2620) covalent geometry : angle 0.67506 ( 3510) hydrogen bonds : bond 0.02676 ( 35) hydrogen bonds : angle 6.80796 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.097 Fit side-chains REVERT: D 337 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7756 (ptp) REVERT: E 323 MET cc_start: 0.7331 (tmm) cc_final: 0.6803 (tmm) REVERT: I 323 MET cc_start: 0.6803 (tpp) cc_final: 0.5581 (pmm) REVERT: I 343 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6858 (mt0) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.0428 time to fit residues: 3.6424 Evaluate side-chains 75 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 343 GLN Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain J residue 322 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 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 = 0.4183 r_free = 0.4183 target = 0.143663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.118898 restraints weight = 6265.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.121593 restraints weight = 3983.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.123494 restraints weight = 2903.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.124810 restraints weight = 2279.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.125873 restraints weight = 1909.331| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 2620 Z= 0.237 Angle : 1.462 59.182 3510 Z= 0.849 Chirality : 0.036 0.150 360 Planarity : 0.004 0.029 470 Dihedral : 5.150 14.727 350 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 5.60 % Allowed : 25.60 % Favored : 68.80 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.91 (0.25), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.19), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 316 TRP 0.007 0.001 TRP F 334 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 2620) covalent geometry : angle 1.46161 ( 3510) hydrogen bonds : bond 0.02758 ( 35) hydrogen bonds : angle 6.81911 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.095 Fit side-chains REVERT: B 323 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7082 (tpp) REVERT: D 337 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7685 (ptp) REVERT: E 323 MET cc_start: 0.7351 (tmm) cc_final: 0.6792 (tmm) REVERT: H 343 GLN cc_start: 0.3681 (OUTLIER) cc_final: 0.2027 (pm20) REVERT: I 323 MET cc_start: 0.6817 (tpp) cc_final: 0.5583 (pmm) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.0414 time to fit residues: 3.4672 Evaluate side-chains 76 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 343 GLN Chi-restraints excluded: chain I residue 319 ASN Chi-restraints excluded: chain J residue 322 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 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 = 0.4182 r_free = 0.4182 target = 0.143620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.118669 restraints weight = 6290.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.121346 restraints weight = 4013.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.123282 restraints weight = 2941.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.124623 restraints weight = 2309.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.125761 restraints weight = 1925.506| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 2620 Z= 0.233 Angle : 1.460 59.014 3510 Z= 0.848 Chirality : 0.036 0.157 360 Planarity : 0.004 0.030 470 Dihedral : 5.150 14.726 350 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 5.20 % Allowed : 26.00 % Favored : 68.80 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.92 (0.25), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.19), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 316 TRP 0.007 0.001 TRP F 334 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 2620) covalent geometry : angle 1.45977 ( 3510) hydrogen bonds : bond 0.02753 ( 35) hydrogen bonds : angle 6.81907 ( 135) =============================================================================== Job complete usr+sys time: 456.96 seconds wall clock time: 8 minutes 32.06 seconds (512.06 seconds total)