Starting phenix.real_space_refine on Mon Feb 10 20:52:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n37_9339/02_2025/6n37_9339.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n37_9339/02_2025/6n37_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_9339/02_2025/6n37_9339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n37_9339/02_2025/6n37_9339.map" model { file = "/net/cci-nas-00/data/ceres_data/6n37_9339/02_2025/6n37_9339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n37_9339/02_2025/6n37_9339.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.02, per 1000 atoms: 0.40 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: 0.54 Conformation dependent library (CDL) restraints added in 300.1 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: 0.37 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: 0.60 Time building geometry restraints manager: 0.66 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.080 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.790 ------------------------------------------------------------------------------- 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= 0.543 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.002 TRP C 334 PHE 0.031 0.008 PHE C 316 *********************** 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 : 0.298 Fit side-chains REVERT: I 336 MET cc_start: 0.8277 (mtm) cc_final: 0.8035 (mtp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1081 time to fit residues: 11.1931 Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.141132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.117340 restraints weight = 6113.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.119894 restraints weight = 3943.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.121718 restraints weight = 2903.092| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2620 Z= 0.275 Angle : 0.768 5.894 3510 Z= 0.397 Chirality : 0.039 0.138 360 Planarity : 0.005 0.033 470 Dihedral : 6.760 18.190 350 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.20 % Allowed : 16.40 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 334 PHE 0.017 0.004 PHE E 316 *********************** 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 72 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.296 Fit side-chains REVERT: B 337 MET cc_start: 0.8263 (ptp) cc_final: 0.8030 (ptp) REVERT: F 340 LEU cc_start: 0.9246 (pt) cc_final: 0.8991 (pp) REVERT: I 336 MET cc_start: 0.7760 (mtm) cc_final: 0.7414 (mtp) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 0.1137 time to fit residues: 9.2560 Evaluate side-chains 64 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain H residue 322 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 19 optimal weight: 0.0470 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 overall best weight: 4.2484 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN C 345 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN G 345 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.145619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.122561 restraints weight = 5988.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.125372 restraints weight = 3696.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.127366 restraints weight = 2667.823| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2620 Z= 0.189 Angle : 0.674 7.030 3510 Z= 0.337 Chirality : 0.036 0.132 360 Planarity : 0.004 0.034 470 Dihedral : 5.826 15.384 350 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.40 % Allowed : 20.80 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 334 PHE 0.013 0.002 PHE A 316 *********************** 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 73 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.308 Fit side-chains REVERT: F 340 LEU cc_start: 0.9041 (pt) cc_final: 0.8830 (pp) REVERT: I 336 MET cc_start: 0.7208 (mtm) cc_final: 0.6778 (mtp) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.1120 time to fit residues: 9.4172 Evaluate side-chains 67 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 E residue 340 LEU Chi-restraints excluded: chain H residue 322 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 40.0000 chunk 18 optimal weight: 0.0870 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 overall best weight: 6.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4161 r_free = 0.4161 target = 0.141351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.117996 restraints weight = 6145.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.120722 restraints weight = 3849.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.122662 restraints weight = 2774.025| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4457 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= 0.227 Angle : 0.660 6.793 3510 Z= 0.335 Chirality : 0.035 0.133 360 Planarity : 0.005 0.034 470 Dihedral : 5.742 15.374 350 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.20 % Allowed : 24.40 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 334 PHE 0.012 0.002 PHE A 316 *********************** 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 70 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.264 Fit side-chains REVERT: I 322 MET cc_start: 0.8050 (mtt) cc_final: 0.7477 (mtt) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.1091 time to fit residues: 8.4752 Evaluate side-chains 66 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 H residue 322 MET Chi-restraints excluded: chain I residue 319 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 40.0000 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.142177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.118598 restraints weight = 6120.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.121319 restraints weight = 3869.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.123175 restraints weight = 2799.971| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4664 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= 0.218 Angle : 0.645 7.016 3510 Z= 0.327 Chirality : 0.035 0.133 360 Planarity : 0.005 0.035 470 Dihedral : 5.565 14.212 350 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.20 % Allowed : 26.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP J 334 PHE 0.012 0.002 PHE A 316 *********************** 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 71 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.246 Fit side-chains REVERT: E 323 MET cc_start: 0.7443 (tmm) cc_final: 0.6946 (tmm) REVERT: F 340 LEU cc_start: 0.9069 (pt) cc_final: 0.8696 (pp) REVERT: I 322 MET cc_start: 0.8068 (mtt) cc_final: 0.7545 (mtt) REVERT: I 323 MET cc_start: 0.6994 (tpp) cc_final: 0.5414 (pmm) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.1088 time to fit residues: 8.6369 Evaluate side-chains 70 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain I residue 319 ASN 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 16 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 22 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 24 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 25 optimal weight: 0.5980 overall best weight: 14.9192 ------------------------------------------------------------------------------- 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** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 345 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 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 = 0.4122 r_free = 0.4122 target = 0.144352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.114620 restraints weight = 6432.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.117233 restraints weight = 4167.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.118966 restraints weight = 3006.101| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 2620 Z= 0.449 Angle : 0.804 5.816 3510 Z= 0.419 Chirality : 0.039 0.133 360 Planarity : 0.005 0.038 470 Dihedral : 6.554 17.520 350 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 29.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 4.80 % Allowed : 27.20 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 334 PHE 0.014 0.003 PHE C 316 *********************** 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: 12 poor density : 61 time to evaluate : 0.265 Fit side-chains REVERT: B 323 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7107 (tpp) REVERT: D 323 MET cc_start: 0.7387 (tpp) cc_final: 0.7182 (tpp) REVERT: F 340 LEU cc_start: 0.9282 (pt) cc_final: 0.9007 (pp) REVERT: H 322 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7752 (mtt) REVERT: I 322 MET cc_start: 0.8306 (mtt) cc_final: 0.7637 (mtt) outliers start: 12 outliers final: 7 residues processed: 63 average time/residue: 0.1064 time to fit residues: 8.4900 Evaluate side-chains 70 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET 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 E residue 319 ASN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain I residue 319 ASN 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 20 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.151411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.121675 restraints weight = 6376.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.124438 restraints weight = 4062.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.126419 restraints weight = 2890.269| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4814 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= 0.231 Angle : 0.698 8.163 3510 Z= 0.347 Chirality : 0.036 0.135 360 Planarity : 0.004 0.037 470 Dihedral : 5.727 14.541 350 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.00 % Allowed : 27.60 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 334 PHE 0.011 0.002 PHE A 316 *********************** 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 73 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.285 Fit side-chains REVERT: D 337 MET cc_start: 0.8126 (ptp) cc_final: 0.7710 (ptp) REVERT: E 323 MET cc_start: 0.7496 (tmm) cc_final: 0.7158 (tmm) REVERT: F 340 LEU cc_start: 0.9189 (pt) cc_final: 0.8956 (pp) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.1109 time to fit residues: 8.8850 Evaluate side-chains 70 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain I residue 319 ASN Chi-restraints excluded: chain I residue 337 MET 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: 9.9990 chunk 26 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 13 optimal weight: 40.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.138727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.114528 restraints weight = 6240.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.117253 restraints weight = 3999.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.119082 restraints weight = 2922.617| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2620 Z= 0.263 Angle : 0.704 6.945 3510 Z= 0.353 Chirality : 0.036 0.135 360 Planarity : 0.004 0.038 470 Dihedral : 5.696 15.203 350 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 3.60 % Allowed : 28.40 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 334 PHE 0.012 0.002 PHE C 316 *********************** 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 72 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.290 Fit side-chains REVERT: B 323 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7138 (tpp) REVERT: D 337 MET cc_start: 0.8108 (ptp) cc_final: 0.7690 (ptp) REVERT: E 323 MET cc_start: 0.7525 (tmm) cc_final: 0.7158 (tmm) REVERT: F 340 LEU cc_start: 0.9206 (pt) cc_final: 0.8971 (pp) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.1019 time to fit residues: 8.1108 Evaluate side-chains 71 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain I residue 319 ASN 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 26 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 3 optimal weight: 10.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- 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** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 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 = 0.4075 r_free = 0.4075 target = 0.136462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.111689 restraints weight = 6334.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.114242 restraints weight = 4127.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.115975 restraints weight = 3044.217| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 2620 Z= 0.406 Angle : 0.788 6.266 3510 Z= 0.408 Chirality : 0.039 0.134 360 Planarity : 0.005 0.040 470 Dihedral : 6.260 15.901 350 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.59 % Favored : 84.41 % Rotamer: Outliers : 4.00 % Allowed : 27.60 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 334 PHE 0.014 0.003 PHE C 316 *********************** 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 72 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.273 Fit side-chains REVERT: B 323 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7094 (tpp) REVERT: E 323 MET cc_start: 0.7374 (tmm) cc_final: 0.7153 (tmm) REVERT: F 340 LEU cc_start: 0.9296 (pt) cc_final: 0.9057 (pp) REVERT: H 322 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7701 (mtt) REVERT: I 337 MET cc_start: 0.8511 (mtm) cc_final: 0.8211 (ptp) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.1027 time to fit residues: 8.0765 Evaluate side-chains 71 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain I residue 319 ASN Chi-restraints excluded: chain J residue 322 MET Chi-restraints excluded: chain J residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4146 r_free = 0.4146 target = 0.138249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.113814 restraints weight = 6178.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.116560 restraints weight = 4001.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.118396 restraints weight = 2923.968| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2620 Z= 0.260 Angle : 0.722 7.264 3510 Z= 0.361 Chirality : 0.037 0.135 360 Planarity : 0.004 0.037 470 Dihedral : 5.722 16.255 350 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 4.00 % Allowed : 28.40 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 334 PHE 0.012 0.002 PHE C 316 ********************** 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 72 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.260 Fit side-chains REVERT: B 323 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7125 (tpp) REVERT: E 323 MET cc_start: 0.7391 (tmm) cc_final: 0.7083 (tmm) REVERT: F 340 LEU cc_start: 0.9205 (pt) cc_final: 0.8994 (pp) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1027 time to fit residues: 8.1446 Evaluate side-chains 70 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain I residue 319 ASN Chi-restraints excluded: chain J residue 322 MET Chi-restraints excluded: chain J residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 28 optimal weight: 40.0000 chunk 19 optimal weight: 40.0000 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 345 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN H 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.141331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.117160 restraints weight = 6189.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.119873 restraints weight = 3961.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.121750 restraints weight = 2891.062| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2620 Z= 0.188 Angle : 0.698 9.023 3510 Z= 0.337 Chirality : 0.037 0.133 360 Planarity : 0.004 0.036 470 Dihedral : 5.252 13.765 350 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 3.20 % Allowed : 29.20 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.24), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.18), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 334 PHE 0.010 0.002 PHE B 316 =============================================================================== Job complete usr+sys time: 873.71 seconds wall clock time: 16 minutes 25.39 seconds (985.39 seconds total)