Starting phenix.real_space_refine on Mon Sep 23 12:32:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/09_2024/6n37_9339.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/09_2024/6n37_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/09_2024/6n37_9339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/09_2024/6n37_9339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/09_2024/6n37_9339.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/09_2024/6n37_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-5461/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: 1.03, 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: 0.65 Conformation dependent library (CDL) restraints added in 349.1 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: 0.34 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: 0.52 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 860 1.34 - 1.45: 450 1.45 - 1.57: 1210 1.57 - 1.69: 0 1.69 - 1.80: 100 Bond restraints: 2620 Sorted by residual: bond pdb=" CB MET H 322 " pdb=" CG MET H 322 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" CB MET F 322 " pdb=" CG MET F 322 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CB MET E 322 " pdb=" CG MET E 322 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CB MET B 322 " pdb=" CG MET B 322 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" CB MET A 322 " pdb=" CG MET A 322 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 ... (remaining 2615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 3013 1.61 - 3.22: 337 3.22 - 4.83: 100 4.83 - 6.43: 30 6.43 - 8.04: 30 Bond angle restraints: 3510 Sorted by residual: angle pdb=" C GLY B 314 " pdb=" N ALA B 315 " pdb=" CA ALA B 315 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C GLY I 314 " pdb=" N ALA I 315 " pdb=" CA ALA I 315 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C GLY G 314 " pdb=" N ALA G 315 " pdb=" CA ALA G 315 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C GLY D 314 " pdb=" N ALA D 315 " pdb=" CA ALA D 315 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C GLY C 314 " pdb=" N ALA C 315 " pdb=" CA ALA C 315 " ideal model delta sigma weight residual 121.54 129.55 -8.01 1.91e+00 2.74e-01 1.76e+01 ... (remaining 3505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.11: 1330 13.11 - 26.23: 180 26.23 - 39.34: 20 39.34 - 52.45: 10 52.45 - 65.56: 30 Dihedral angle restraints: 1570 sinusoidal: 560 harmonic: 1010 Sorted by residual: dihedral pdb=" CA GLY D 314 " pdb=" C GLY D 314 " pdb=" N ALA D 315 " pdb=" CA ALA D 315 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY E 314 " pdb=" C GLY E 314 " pdb=" N ALA E 315 " pdb=" CA ALA E 315 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY F 314 " pdb=" C GLY F 314 " pdb=" N ALA F 315 " pdb=" CA ALA F 315 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 1567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 186 0.033 - 0.066: 64 0.066 - 0.099: 70 0.099 - 0.132: 14 0.132 - 0.165: 26 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA PHE C 316 " pdb=" N PHE C 316 " pdb=" C PHE C 316 " pdb=" CB PHE C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA PHE J 316 " pdb=" N PHE J 316 " pdb=" C PHE J 316 " pdb=" CB PHE J 316 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA PHE D 316 " pdb=" N PHE D 316 " pdb=" C PHE D 316 " pdb=" CB PHE D 316 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 357 not shown) Planarity restraints: 470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY J 314 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLY J 314 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY J 314 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA J 315 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 314 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLY B 314 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY B 314 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA B 315 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 314 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.46e+01 pdb=" C GLY H 314 " 0.066 2.00e-02 2.50e+03 pdb=" O GLY H 314 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA H 315 " -0.022 2.00e-02 2.50e+03 ... (remaining 467 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1018 2.90 - 3.40: 2308 3.40 - 3.90: 4160 3.90 - 4.40: 4564 4.40 - 4.90: 9139 Nonbonded interactions: 21189 Sorted by model distance: nonbonded pdb=" N ASN J 319 " pdb=" OD1 ASN J 319 " model vdw 2.399 3.120 nonbonded pdb=" N ASN H 319 " pdb=" OD1 ASN H 319 " model vdw 2.399 3.120 nonbonded pdb=" N ASN G 319 " pdb=" OD1 ASN G 319 " model vdw 2.399 3.120 nonbonded pdb=" N ASN B 319 " pdb=" OD1 ASN B 319 " model vdw 2.400 3.120 nonbonded pdb=" N ASN E 319 " pdb=" OD1 ASN E 319 " model vdw 2.400 3.120 ... (remaining 21184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.010 Find NCS groups from input model: 0.090 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.289 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: 0.1090 time to fit residues: 11.2268 Evaluate side-chains 59 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.294 Fit side-chains REVERT: B 337 MET cc_start: 0.8441 (ptp) cc_final: 0.8156 (ptp) REVERT: F 340 LEU cc_start: 0.9249 (pt) cc_final: 0.9014 (pp) REVERT: I 336 MET cc_start: 0.7777 (mtm) cc_final: 0.7420 (mtp) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 0.1105 time to fit residues: 9.0934 Evaluate side-chains 64 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 22 optimal weight: 40.0000 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 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 345 ASN ** G 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 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4166 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= 0.255 Angle : 0.711 6.929 3510 Z= 0.360 Chirality : 0.037 0.134 360 Planarity : 0.005 0.036 470 Dihedral : 6.227 17.141 350 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.40 % Allowed : 22.40 % Favored : 75.20 % 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: -5.10 (0.21), 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 0.010 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 69 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.277 Fit side-chains REVERT: C 322 MET cc_start: 0.8044 (mtt) cc_final: 0.7664 (mtt) REVERT: I 337 MET cc_start: 0.8314 (ptp) cc_final: 0.8079 (ptp) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.1063 time to fit residues: 8.4000 Evaluate side-chains 64 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 optimal weight: 40.0000 chunk 13 optimal weight: 0.0060 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 0.4980 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 40.0000 chunk 24 optimal weight: 30.0000 chunk 16 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 overall best weight: 5.5004 ------------------------------------------------------------------------------- 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 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** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4556 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= 0.206 Angle : 0.655 6.961 3510 Z= 0.333 Chirality : 0.036 0.134 360 Planarity : 0.005 0.034 470 Dihedral : 5.790 15.239 350 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.40 % Allowed : 24.00 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.009 0.002 TRP G 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 73 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: C 322 MET cc_start: 0.8018 (mtt) cc_final: 0.7791 (mtt) outliers start: 11 outliers final: 4 residues processed: 63 average time/residue: 0.1047 time to fit residues: 8.3470 Evaluate side-chains 65 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain F 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 21 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 24 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- 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** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2620 Z= 0.259 Angle : 0.662 6.743 3510 Z= 0.342 Chirality : 0.035 0.136 360 Planarity : 0.005 0.035 470 Dihedral : 5.868 15.133 350 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.40 % Allowed : 27.60 % 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: -5.07 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 334 PHE 0.012 0.002 PHE C 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 66 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.255 Fit side-chains REVERT: B 337 MET cc_start: 0.8201 (ptp) cc_final: 0.7938 (mtm) REVERT: D 323 MET cc_start: 0.7400 (tpp) cc_final: 0.7082 (tpp) REVERT: D 337 MET cc_start: 0.8290 (ptp) cc_final: 0.7961 (ptp) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.1106 time to fit residues: 8.3151 Evaluate side-chains 65 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 J residue 322 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2620 Z= 0.227 Angle : 0.654 7.023 3510 Z= 0.331 Chirality : 0.035 0.135 360 Planarity : 0.004 0.034 470 Dihedral : 5.631 14.265 350 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 4.80 % Allowed : 26.40 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.01 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 334 PHE 0.011 0.002 PHE A 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 74 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.220 Fit side-chains REVERT: D 323 MET cc_start: 0.7415 (tpp) cc_final: 0.7112 (tpp) REVERT: I 322 MET cc_start: 0.8176 (mtt) cc_final: 0.7976 (mtt) REVERT: I 323 MET cc_start: 0.6970 (tpp) cc_final: 0.5447 (pmm) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.1024 time to fit residues: 8.1992 Evaluate side-chains 70 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 343 GLN Chi-restraints excluded: chain I residue 319 ASN Chi-restraints excluded: chain J residue 322 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2620 Z= 0.195 Angle : 0.652 8.272 3510 Z= 0.321 Chirality : 0.035 0.133 360 Planarity : 0.004 0.033 470 Dihedral : 5.336 13.887 350 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 4.00 % Allowed : 26.00 % 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: -4.95 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.18), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 334 PHE 0.010 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 72 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.272 Fit side-chains REVERT: B 323 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6855 (tpp) REVERT: I 323 MET cc_start: 0.6901 (tpp) cc_final: 0.5206 (pmm) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.1076 time to fit residues: 8.4939 Evaluate side-chains 68 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 340 LEU Chi-restraints excluded: chain G residue 319 ASN Chi-restraints excluded: chain H residue 322 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 2 optimal weight: 40.0000 chunk 22 optimal weight: 40.0000 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 24 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 overall best weight: 12.1994 ------------------------------------------------------------------------------- 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 A 345 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 345 ASN G 343 GLN G 345 ASN I 343 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4842 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= 0.379 Angle : 0.760 7.381 3510 Z= 0.389 Chirality : 0.037 0.132 360 Planarity : 0.004 0.033 470 Dihedral : 6.143 15.439 350 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 5.20 % Allowed : 25.60 % Favored : 69.20 % 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: -5.16 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.17), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP G 334 PHE 0.012 0.003 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 75 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.282 Fit side-chains REVERT: B 323 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: D 323 MET cc_start: 0.7390 (tpp) cc_final: 0.7107 (tpp) REVERT: I 323 MET cc_start: 0.7099 (tpp) cc_final: 0.5434 (pmm) REVERT: I 337 MET cc_start: 0.8275 (mtm) cc_final: 0.7990 (mtm) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.1081 time to fit residues: 8.8985 Evaluate side-chains 72 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 340 LEU Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain F 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 28 optimal weight: 40.0000 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 overall best weight: 3.0724 ------------------------------------------------------------------------------- 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 345 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN G 345 ASN H 343 GLN I 343 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.002 0.020 2620 Z= 0.147 Angle : 0.650 7.781 3510 Z= 0.317 Chirality : 0.035 0.134 360 Planarity : 0.004 0.031 470 Dihedral : 5.138 14.633 350 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.00 % Allowed : 26.80 % Favored : 69.20 % 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: -4.99 (0.24), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.18), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 334 PHE 0.008 0.001 PHE B 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 76 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.253 Fit side-chains REVERT: B 323 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6958 (tpp) REVERT: I 322 MET cc_start: 0.7809 (mtt) cc_final: 0.7532 (mtt) REVERT: I 323 MET cc_start: 0.6783 (tpp) cc_final: 0.5461 (pmm) REVERT: I 337 MET cc_start: 0.7990 (mtm) cc_final: 0.7170 (mtm) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.1041 time to fit residues: 8.8966 Evaluate side-chains 69 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 340 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 30.0000 chunk 21 optimal weight: 30.0000 chunk 3 optimal weight: 40.0000 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- 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 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 345 ASN G 343 GLN G 345 ASN H 343 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5006 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= 0.302 Angle : 0.736 8.249 3510 Z= 0.365 Chirality : 0.036 0.133 360 Planarity : 0.004 0.030 470 Dihedral : 5.688 16.595 350 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % 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: -5.01 (0.24), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.19), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 334 PHE 0.011 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 fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.289 Fit side-chains REVERT: B 323 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6986 (tpp) REVERT: D 323 MET cc_start: 0.7332 (tpp) cc_final: 0.7050 (tpp) REVERT: I 323 MET cc_start: 0.6980 (tpp) cc_final: 0.5507 (pmm) REVERT: I 336 MET cc_start: 0.5731 (mmm) cc_final: 0.4241 (ppp) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1106 time to fit residues: 8.7669 Evaluate side-chains 70 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 340 LEU Chi-restraints excluded: chain E residue 343 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 20.0000 chunk 18 optimal weight: 0.0980 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 331 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.4156 r_free = 0.4156 target = 0.137864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.113635 restraints weight = 6181.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.116212 restraints weight = 4025.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.117934 restraints weight = 2954.801| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 2620 Z= 0.450 Angle : 1.594 59.152 3510 Z= 0.914 Chirality : 0.061 0.906 360 Planarity : 0.004 0.030 470 Dihedral : 5.706 17.366 350 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 3.20 % Allowed : 28.40 % Favored : 68.40 % Cbeta Deviations : 0.30 % 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 (0.24), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.19), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 334 PHE 0.011 0.002 PHE C 316 =============================================================================== Job complete usr+sys time: 752.77 seconds wall clock time: 14 minutes 3.52 seconds (843.52 seconds total)