Starting phenix.real_space_refine on Sat Apr 26 16:39:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n37_9339/04_2025/6n37_9339.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n37_9339/04_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_9339/04_2025/6n37_9339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n37_9339/04_2025/6n37_9339.map" model { file = "/net/cci-nas-00/data/ceres_data/6n37_9339/04_2025/6n37_9339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n37_9339/04_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-5669/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: 1.17, per 1000 atoms: 0.45 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: 0.63 Conformation dependent library (CDL) restraints added in 347.1 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: 0.36 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: 0.54 Time building geometry restraints manager: 0.75 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: 0.110 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.25003 ( 35) hydrogen bonds : angle 10.72751 ( 135) covalent geometry : bond 0.00867 ( 2620) covalent geometry : angle 1.41889 ( 3510) *********************** 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 : 0.276 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: 0.1119 time to fit residues: 11.5305 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 : 0.280 ------------------------------------------------------------------------------- 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= 0.206 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 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 35) hydrogen bonds : angle 8.07078 ( 135) covalent geometry : bond 0.00434 ( 2620) covalent geometry : angle 0.76793 ( 3510) *********************** 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 : 0.301 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: 0.1141 time to fit residues: 9.2652 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 : 0.299 ------------------------------------------------------------------------------- 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: 30.0000 chunk 19 optimal weight: 0.0470 chunk 7 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 overall best weight: 4.4284 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.145174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.122083 restraints weight = 6003.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.124924 restraints weight = 3707.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.126933 restraints weight = 2647.474| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4205 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= 0.145 Angle : 0.676 6.748 3510 Z= 0.340 Chirality : 0.036 0.132 360 Planarity : 0.005 0.034 470 Dihedral : 5.867 15.586 350 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.40 % Allowed : 21.60 % Favored : 76.00 % 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: -5.05 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 334 PHE 0.013 0.002 PHE A 316 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 35) hydrogen bonds : angle 7.36578 ( 135) covalent geometry : bond 0.00309 ( 2620) covalent geometry : angle 0.67567 ( 3510) *********************** 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 72 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.301 Fit side-chains REVERT: F 340 LEU cc_start: 0.9046 (pt) cc_final: 0.8833 (pp) REVERT: I 336 MET cc_start: 0.7222 (mtm) cc_final: 0.6816 (mtp) REVERT: I 337 MET cc_start: 0.8153 (ptp) cc_final: 0.7909 (ptp) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.1108 time to fit residues: 9.1470 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 : 0.267 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 40.0000 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 ** 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 = 0.4139 r_free = 0.4139 target = 0.139213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.115591 restraints weight = 6213.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.118291 restraints weight = 3883.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.120149 restraints weight = 2816.055| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4389 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= 0.205 Angle : 0.692 6.602 3510 Z= 0.353 Chirality : 0.036 0.133 360 Planarity : 0.005 0.036 470 Dihedral : 6.022 16.415 350 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 2.80 % Allowed : 24.80 % 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: -5.14 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 334 PHE 0.013 0.002 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.02839 ( 35) hydrogen bonds : angle 7.32710 ( 135) covalent geometry : bond 0.00434 ( 2620) covalent geometry : angle 0.69166 ( 3510) *********************** 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 67 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.298 Fit side-chains REVERT: D 323 MET cc_start: 0.7479 (tpp) cc_final: 0.7176 (tpp) REVERT: I 336 MET cc_start: 0.7077 (mtm) cc_final: 0.6270 (mtp) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.1110 time to fit residues: 8.5344 Evaluate side-chains 64 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 40.0000 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 345 ASN ** 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 = 0.4169 r_free = 0.4169 target = 0.142371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.118663 restraints weight = 6112.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.121370 restraints weight = 3855.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.123299 restraints weight = 2800.690| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4642 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= 0.157 Angle : 0.655 7.149 3510 Z= 0.329 Chirality : 0.035 0.134 360 Planarity : 0.005 0.036 470 Dihedral : 5.629 14.352 350 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.60 % Allowed : 26.40 % 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: -5.10 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.16), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 334 PHE 0.012 0.002 PHE A 316 Details of bonding type rmsd hydrogen bonds : bond 0.02640 ( 35) hydrogen bonds : angle 7.09089 ( 135) covalent geometry : bond 0.00339 ( 2620) covalent geometry : angle 0.65450 ( 3510) *********************** 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: 9 poor density : 62 time to evaluate : 0.270 Fit side-chains REVERT: D 323 MET cc_start: 0.7464 (tpp) cc_final: 0.7183 (tpp) REVERT: E 323 MET cc_start: 0.7457 (tmm) cc_final: 0.6977 (tmm) REVERT: F 340 LEU cc_start: 0.9074 (pt) cc_final: 0.8690 (pp) REVERT: G 343 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7026 (tp-100) outliers start: 9 outliers final: 4 residues processed: 63 average time/residue: 0.1063 time to fit residues: 8.3890 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain H residue 322 MET 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: 40.0000 chunk 2 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 overall best weight: 10.3992 ------------------------------------------------------------------------------- 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** ** 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** ** 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** ** 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 = 0.4113 r_free = 0.4113 target = 0.139898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.115261 restraints weight = 6348.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.117808 restraints weight = 4142.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.119484 restraints weight = 3044.393| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2620 Z= 0.246 Angle : 0.714 6.447 3510 Z= 0.369 Chirality : 0.037 0.133 360 Planarity : 0.005 0.037 470 Dihedral : 6.108 15.409 350 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 4.00 % Allowed : 27.20 % 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 (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: -5.15 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 334 PHE 0.012 0.002 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 35) hydrogen bonds : angle 7.23280 ( 135) covalent geometry : bond 0.00520 ( 2620) covalent geometry : angle 0.71418 ( 3510) *********************** 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 71 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.304 Fit side-chains REVERT: D 323 MET cc_start: 0.7464 (tpp) cc_final: 0.7214 (tpp) REVERT: E 323 MET cc_start: 0.7448 (tmm) cc_final: 0.7208 (tmm) REVERT: F 340 LEU cc_start: 0.9246 (pt) cc_final: 0.8962 (pp) REVERT: G 343 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7252 (tp-100) outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.1112 time to fit residues: 8.8011 Evaluate side-chains 67 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain G residue 343 GLN 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: 10.0000 chunk 15 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** 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 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 = 0.4170 r_free = 0.4170 target = 0.141372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.117241 restraints weight = 6256.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.119972 restraints weight = 4018.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.121908 restraints weight = 2922.103| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2620 Z= 0.148 Angle : 0.671 8.227 3510 Z= 0.331 Chirality : 0.036 0.135 360 Planarity : 0.004 0.036 470 Dihedral : 5.506 14.615 350 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.40 % Allowed : 28.40 % Favored : 67.20 % 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: -5.09 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 334 PHE 0.011 0.002 PHE A 316 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 35) hydrogen bonds : angle 6.91308 ( 135) covalent geometry : bond 0.00319 ( 2620) covalent geometry : angle 0.67109 ( 3510) *********************** 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: 11 poor density : 62 time to evaluate : 0.270 Fit side-chains REVERT: B 323 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7076 (tpp) REVERT: D 323 MET cc_start: 0.7368 (tpp) cc_final: 0.7157 (tpp) REVERT: D 337 MET cc_start: 0.8079 (ptp) cc_final: 0.7771 (ptp) REVERT: E 323 MET cc_start: 0.7423 (tmm) cc_final: 0.7144 (tmm) REVERT: F 340 LEU cc_start: 0.9167 (pt) cc_final: 0.8907 (pp) REVERT: G 343 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7085 (tp-100) REVERT: I 323 MET cc_start: 0.7130 (tpp) cc_final: 0.6902 (tpp) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 0.1038 time to fit residues: 8.3504 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 : 0.282 ------------------------------------------------------------------------------- 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 G residue 319 ASN Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H 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: 10.0000 chunk 26 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 10 optimal weight: 40.0000 chunk 5 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** 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 = 0.4172 r_free = 0.4172 target = 0.148208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.118141 restraints weight = 6352.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.120857 restraints weight = 4091.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.122708 restraints weight = 2918.521| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2620 Z= 0.257 Angle : 0.758 8.127 3510 Z= 0.379 Chirality : 0.037 0.133 360 Planarity : 0.005 0.037 470 Dihedral : 5.959 14.858 350 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 4.40 % Allowed : 28.00 % 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: -5.18 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.18), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 334 PHE 0.012 0.002 PHE A 316 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 35) hydrogen bonds : angle 7.18827 ( 135) covalent geometry : bond 0.00542 ( 2620) covalent geometry : angle 0.75797 ( 3510) *********************** 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 74 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.273 Fit side-chains REVERT: B 323 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7122 (tpp) REVERT: D 323 MET cc_start: 0.7433 (tpp) cc_final: 0.7183 (tpp) REVERT: E 323 MET cc_start: 0.7432 (tmm) cc_final: 0.7206 (tmm) REVERT: F 340 LEU cc_start: 0.9255 (pt) cc_final: 0.9005 (pp) REVERT: G 343 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7385 (tp-100) REVERT: I 322 MET cc_start: 0.8111 (mtt) cc_final: 0.7712 (mtt) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.1053 time to fit residues: 8.4537 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 : 0.278 ------------------------------------------------------------------------------- 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 E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain G residue 343 GLN 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: 9.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 40.0000 chunk 16 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 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 = 0.4070 r_free = 0.4070 target = 0.135952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.111465 restraints weight = 6333.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.113975 restraints weight = 4132.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.115619 restraints weight = 3067.410| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 2620 Z= 0.296 Angle : 0.813 7.837 3510 Z= 0.410 Chirality : 0.039 0.135 360 Planarity : 0.004 0.037 470 Dihedral : 6.283 15.896 350 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.59 % Favored : 84.41 % Rotamer: Outliers : 4.00 % Allowed : 29.20 % Favored : 66.80 % 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: -5.32 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP G 334 PHE 0.014 0.003 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 35) hydrogen bonds : angle 7.34922 ( 135) covalent geometry : bond 0.00625 ( 2620) covalent geometry : angle 0.81265 ( 3510) *********************** 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 73 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.287 Fit side-chains REVERT: B 323 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6953 (tpp) REVERT: D 323 MET cc_start: 0.7331 (tpp) cc_final: 0.7117 (tpp) REVERT: E 323 MET cc_start: 0.7356 (tmm) cc_final: 0.7153 (tmm) REVERT: F 340 LEU cc_start: 0.9304 (pt) cc_final: 0.9090 (pp) REVERT: G 343 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7490 (tp-100) REVERT: I 322 MET cc_start: 0.8205 (mtt) cc_final: 0.7919 (mtt) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.1083 time to fit residues: 8.6906 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 : 0.272 ------------------------------------------------------------------------------- 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 E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain G residue 343 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.137388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.113124 restraints weight = 6212.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.115797 restraints weight = 4012.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.117619 restraints weight = 2930.593| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2620 Z= 0.194 Angle : 0.740 7.735 3510 Z= 0.364 Chirality : 0.037 0.135 360 Planarity : 0.004 0.035 470 Dihedral : 5.781 14.665 350 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 3.60 % Allowed : 30.00 % Favored : 66.40 % 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: -5.23 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 334 PHE 0.012 0.002 PHE A 316 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 35) hydrogen bonds : angle 7.20740 ( 135) covalent geometry : bond 0.00416 ( 2620) covalent geometry : angle 0.73951 ( 3510) ********************** 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: 9 poor density : 63 time to evaluate : 0.285 Fit side-chains REVERT: B 323 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7096 (tpp) REVERT: E 323 MET cc_start: 0.7455 (tmm) cc_final: 0.7238 (tmm) REVERT: F 340 LEU cc_start: 0.9215 (pt) cc_final: 0.9007 (pp) REVERT: G 343 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7190 (tp-100) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 0.1123 time to fit residues: 8.9905 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 : 0.292 ------------------------------------------------------------------------------- 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 G residue 319 ASN Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain H residue 322 MET 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 26 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN 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 ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.144309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.119905 restraints weight = 6168.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.122631 restraints weight = 3956.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.124399 restraints weight = 2893.195| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5243 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= 0.127 Angle : 0.698 7.580 3510 Z= 0.336 Chirality : 0.037 0.133 360 Planarity : 0.004 0.033 470 Dihedral : 5.190 14.676 350 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.60 % Allowed : 29.60 % Favored : 66.80 % 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: -5.08 (0.24), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.18), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 334 PHE 0.010 0.002 PHE A 316 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 35) hydrogen bonds : angle 6.91560 ( 135) covalent geometry : bond 0.00276 ( 2620) covalent geometry : angle 0.69782 ( 3510) =============================================================================== Job complete usr+sys time: 979.03 seconds wall clock time: 17 minutes 42.19 seconds (1062.19 seconds total)