Starting phenix.real_space_refine (version: dev) on Thu Feb 16 23:26:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/02_2023/6n37_9339.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/02_2023/6n37_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_9339/02_2023/6n37_9339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/02_2023/6n37_9339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/02_2023/6n37_9339.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n37_9339/02_2023/6n37_9339.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 2580 Number of models: 1 Model: "" Number of chains: 10 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} Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "C" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "D" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "E" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "G" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "H" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "I" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "J" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 258 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Time building chain proxies: 1.69, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 0.99 Conformation dependent library (CDL) restraints added in 489.9 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: 0.16 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: 1.08 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: 99.45 - 106.34: 100 106.34 - 113.24: 1290 113.24 - 120.14: 831 120.14 - 127.04: 1249 127.04 - 133.93: 40 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 2.520 nonbonded pdb=" N ASN H 319 " pdb=" OD1 ASN H 319 " model vdw 2.399 2.520 nonbonded pdb=" N ASN G 319 " pdb=" OD1 ASN G 319 " model vdw 2.399 2.520 nonbonded pdb=" N ASN B 319 " pdb=" OD1 ASN B 319 " model vdw 2.400 2.520 nonbonded pdb=" N ASN E 319 " pdb=" OD1 ASN E 319 " model vdw 2.400 2.520 ... (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 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 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. 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: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.040 Process input model: 11.630 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 % 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 *********************** 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 : 0.312 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1101 time to fit residues: 11.3809 Evaluate side-chains 59 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3875 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN C 343 GLN C 345 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** 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 345 ASN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN J 345 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3659 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= 0.242 Angle : 0.734 6.338 3510 Z= 0.377 Chirality : 0.038 0.131 360 Planarity : 0.005 0.031 470 Dihedral : 6.496 17.853 350 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 8.00 % 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: -5.29 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.16), residues: 340 *********************** 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 85 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.296 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 77 average time/residue: 0.1015 time to fit residues: 9.7697 Evaluate side-chains 72 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.253 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0282 time to fit residues: 0.9343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 7 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 345 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 2620 Z= 0.233 Angle : 0.693 8.598 3510 Z= 0.347 Chirality : 0.036 0.136 360 Planarity : 0.005 0.032 470 Dihedral : 5.968 16.300 350 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 3.20 % 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: -5.21 (0.20), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.15), residues: 340 *********************** 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 70 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.271 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.1073 time to fit residues: 9.0008 Evaluate side-chains 66 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0356 time to fit residues: 0.6182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 40.0000 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 overall best weight: 17.3998 ------------------------------------------------------------------------------- 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** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.059 2620 Z= 0.521 Angle : 0.852 5.481 3510 Z= 0.452 Chirality : 0.040 0.133 360 Planarity : 0.006 0.038 470 Dihedral : 7.286 19.704 350 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 31.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer Outliers : 6.00 % 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: -5.67 (0.18), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.14), residues: 340 *********************** 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 72 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.288 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 65 average time/residue: 0.1159 time to fit residues: 9.4110 Evaluate side-chains 69 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0328 time to fit residues: 1.0283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4632 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= 0.242 Angle : 0.679 6.831 3510 Z= 0.347 Chirality : 0.036 0.139 360 Planarity : 0.005 0.037 470 Dihedral : 6.044 16.235 350 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer Outliers : 2.00 % 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: -5.57 (0.19), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.15), residues: 340 *********************** 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: 5 poor density : 61 time to evaluate : 0.295 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 0.1109 time to fit residues: 8.5387 Evaluate side-chains 62 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0537 time to fit residues: 0.4445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4772 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= 0.219 Angle : 0.683 9.076 3510 Z= 0.336 Chirality : 0.036 0.138 360 Planarity : 0.005 0.035 470 Dihedral : 5.675 15.020 350 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer Outliers : 4.00 % 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: -5.53 (0.20), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.15), residues: 340 *********************** 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 fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.291 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.1030 time to fit residues: 8.6428 Evaluate side-chains 69 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0280 time to fit residues: 0.6176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** ** B 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 2620 Z= 0.170 Angle : 0.658 8.754 3510 Z= 0.318 Chirality : 0.036 0.139 360 Planarity : 0.004 0.034 470 Dihedral : 5.255 14.309 350 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 3.20 % 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: -5.42 (0.20), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.15), residues: 340 *********************** 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: 8 poor density : 64 time to evaluate : 0.309 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.1087 time to fit residues: 9.2493 Evaluate side-chains 70 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0369 time to fit residues: 0.8707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 26 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 40.0000 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 8 optimal weight: 30.0000 chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 H 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5100 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= 0.149 Angle : 0.659 9.419 3510 Z= 0.309 Chirality : 0.036 0.133 360 Planarity : 0.004 0.030 470 Dihedral : 4.941 15.090 350 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 1.60 % 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: -5.24 (0.21), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.16), residues: 340 *********************** 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 73 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.260 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.1107 time to fit residues: 9.5943 Evaluate side-chains 66 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0512 time to fit residues: 0.6184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 13 optimal weight: 40.0000 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.0470 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 overall best weight: 6.8086 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 2620 Z= 0.235 Angle : 0.681 7.696 3510 Z= 0.334 Chirality : 0.036 0.131 360 Planarity : 0.004 0.030 470 Dihedral : 5.331 14.465 350 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer Outliers : 1.20 % 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: -5.21 (0.22), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.17), residues: 340 *********************** 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 66 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.293 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 0.1173 time to fit residues: 9.2436 Evaluate side-chains 66 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0280 time to fit residues: 0.5166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 3 optimal weight: 40.0000 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 0.0980 chunk 4 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 overall best weight: 7.8190 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5077 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= 0.261 Angle : 0.698 7.307 3510 Z= 0.345 Chirality : 0.036 0.132 360 Planarity : 0.004 0.030 470 Dihedral : 5.525 14.147 350 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer Outliers : 0.80 % 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: -5.20 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.17), residues: 340 ********************** 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 65 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.315 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 0.1024 time to fit residues: 8.4088 Evaluate side-chains 63 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 28 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.141210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.116226 restraints weight = 6184.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.118805 restraints weight = 4071.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.120701 restraints weight = 3034.648| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5137 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= 0.219 Angle : 0.702 9.159 3510 Z= 0.337 Chirality : 0.035 0.133 360 Planarity : 0.004 0.029 470 Dihedral : 5.327 14.414 350 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer Outliers : 1.20 % 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: -5.15 (0.23), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.17), residues: 340 =============================================================================== Job complete usr+sys time: 704.26 seconds wall clock time: 13 minutes 37.89 seconds (817.89 seconds total)