Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 18:58:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/07_2023/7s9d_24933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/07_2023/7s9d_24933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/07_2023/7s9d_24933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/07_2023/7s9d_24933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/07_2023/7s9d_24933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/07_2023/7s9d_24933.pdb" } resolution = 4.6 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= 0.003 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 6860 2.51 5 N 1682 2.21 5 O 1870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 10462 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5231 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 1 Chain: "B" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5231 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 1 Time building chain proxies: 5.25, per 1000 atoms: 0.50 Number of scatterers: 10462 At special positions: 0 Unit cell: (115.867, 111.615, 112.678, 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 1870 8.00 N 1682 7.00 C 6860 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: 4.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 61.9% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 77 through 105 Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 126 removed outlier: 4.176A pdb=" N GLY A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.612A pdb=" N SER A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.124A pdb=" N LEU A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 228 removed outlier: 3.718A pdb=" N VAL A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 removed outlier: 3.541A pdb=" N ASN A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 282 removed outlier: 3.867A pdb=" N PHE A 282 " --> pdb=" O PHE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.790A pdb=" N VAL A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 363 Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 398 through 406 Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.563A pdb=" N PHE A 432 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.759A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 503 Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 563 through 581 removed outlier: 3.514A pdb=" N LYS A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 671 Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 77 through 105 Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 108 through 126 removed outlier: 4.177A pdb=" N GLY B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 137 through 151 removed outlier: 3.611A pdb=" N SER B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 199 through 205 removed outlier: 4.125A pdb=" N LEU B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 228 removed outlier: 3.716A pdb=" N VAL B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.542A pdb=" N ASN B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 282 removed outlier: 3.868A pdb=" N PHE B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 306 removed outlier: 3.791A pdb=" N VAL B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 363 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.564A pdb=" N PHE B 432 " --> pdb=" O GLY B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 453 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 465 through 482 removed outlier: 3.759A pdb=" N LEU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 563 through 581 removed outlier: 3.514A pdb=" N LYS B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 671 Processing helix chain 'B' and resid 681 through 690 Processing helix chain 'B' and resid 698 through 700 No H-bonds generated for 'chain 'B' and resid 698 through 700' Processing helix chain 'B' and resid 705 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 535 through 539 removed outlier: 6.230A pdb=" N ILE A 642 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA A 677 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 644 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 535 through 539 removed outlier: 6.230A pdb=" N ILE B 642 " --> pdb=" O TYR B 675 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA B 677 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 644 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1788 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: 2.92 Time building geometry restraints manager: 4.74 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: 3240 1.34 - 1.46: 2515 1.46 - 1.58: 4861 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 10698 Sorted by residual: bond pdb=" CA SER B 400 " pdb=" CB SER B 400 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.05e+01 bond pdb=" CA SER A 400 " pdb=" CB SER A 400 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 bond pdb=" N PHE A 137 " pdb=" CA PHE A 137 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.05e+00 bond pdb=" N PHE B 137 " pdb=" CA PHE B 137 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.19e-02 7.06e+03 6.96e+00 bond pdb=" N VAL A 139 " pdb=" CA VAL A 139 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.24e-02 6.50e+03 5.42e+00 ... (remaining 10693 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.17: 238 105.17 - 112.35: 5688 112.35 - 119.53: 3259 119.53 - 126.70: 5254 126.70 - 133.88: 101 Bond angle restraints: 14540 Sorted by residual: angle pdb=" N LEU B 397 " pdb=" CA LEU B 397 " pdb=" C LEU B 397 " ideal model delta sigma weight residual 113.88 106.31 7.57 1.23e+00 6.61e-01 3.78e+01 angle pdb=" N LEU A 397 " pdb=" CA LEU A 397 " pdb=" C LEU A 397 " ideal model delta sigma weight residual 113.88 106.33 7.55 1.23e+00 6.61e-01 3.77e+01 angle pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta sigma weight residual 121.54 112.05 9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta sigma weight residual 121.54 112.05 9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" CB MET B 180 " pdb=" CG MET B 180 " pdb=" SD MET B 180 " ideal model delta sigma weight residual 112.70 98.00 14.70 3.00e+00 1.11e-01 2.40e+01 ... (remaining 14535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.57: 5572 12.57 - 25.14: 582 25.14 - 37.71: 148 37.71 - 50.28: 30 50.28 - 62.84: 6 Dihedral angle restraints: 6338 sinusoidal: 2432 harmonic: 3906 Sorted by residual: dihedral pdb=" CA SER A 24 " pdb=" C SER A 24 " pdb=" N HIS A 25 " pdb=" CA HIS A 25 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA SER B 24 " pdb=" C SER B 24 " pdb=" N HIS B 25 " pdb=" CA HIS B 25 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR A 616 " pdb=" C TYR A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 6335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1079 0.039 - 0.077: 462 0.077 - 0.115: 155 0.115 - 0.154: 20 0.154 - 0.192: 10 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA LEU A 397 " pdb=" N LEU A 397 " pdb=" C LEU A 397 " pdb=" CB LEU A 397 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA LEU B 397 " pdb=" N LEU B 397 " pdb=" C LEU B 397 " pdb=" CB LEU B 397 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CG LEU A 28 " pdb=" CB LEU A 28 " pdb=" CD1 LEU A 28 " pdb=" CD2 LEU A 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1723 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 136 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C PRO A 136 " -0.032 2.00e-02 2.50e+03 pdb=" O PRO A 136 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 137 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 136 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PRO B 136 " -0.030 2.00e-02 2.50e+03 pdb=" O PRO B 136 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE B 137 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 394 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C SER A 394 " 0.028 2.00e-02 2.50e+03 pdb=" O SER A 394 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS A 395 " -0.010 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 282 2.66 - 3.22: 11872 3.22 - 3.78: 17632 3.78 - 4.34: 22681 4.34 - 4.90: 34822 Nonbonded interactions: 87289 Sorted by model distance: nonbonded pdb=" NZ LYS A 227 " pdb=" OG1 THR A 234 " model vdw 2.095 2.520 nonbonded pdb=" NZ LYS B 227 " pdb=" OG1 THR B 234 " model vdw 2.096 2.520 nonbonded pdb=" O THR A 234 " pdb=" NH1 ARG A 236 " model vdw 2.100 2.520 nonbonded pdb=" O THR B 234 " pdb=" NH1 ARG B 236 " model vdw 2.100 2.520 nonbonded pdb=" O PHE A 460 " pdb=" OG1 THR A 464 " model vdw 2.103 2.440 ... (remaining 87284 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' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 0.850 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: 4.390 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 28.680 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.006 0.051 10698 Z= 0.421 Angle : 0.888 14.704 14540 Z= 0.522 Chirality : 0.047 0.192 1726 Planarity : 0.005 0.039 1812 Dihedral : 11.266 62.844 3838 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.70 % Favored : 89.00 % Rotamer Outliers : 0.35 % 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: -0.95 (0.23), residues: 1346 helix: 0.66 (0.18), residues: 828 sheet: 1.65 (0.83), residues: 38 loop : -3.27 (0.25), residues: 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.650 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.1536 time to fit residues: 7.2163 Evaluate side-chains 26 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4991 time to fit residues: 1.3519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.0970 chunk 78 optimal weight: 0.2980 chunk 121 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN A 689 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10698 Z= 0.179 Angle : 0.585 8.645 14540 Z= 0.294 Chirality : 0.043 0.187 1726 Planarity : 0.004 0.054 1812 Dihedral : 4.484 29.212 1448 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.43 % Favored : 92.42 % Rotamer Outliers : 0.17 % 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: -0.31 (0.23), residues: 1346 helix: 1.21 (0.18), residues: 824 sheet: 2.49 (0.81), residues: 36 loop : -3.10 (0.25), residues: 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.623 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1190 time to fit residues: 7.0795 Evaluate side-chains 30 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 108 optimal weight: 0.0020 chunk 120 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10698 Z= 0.170 Angle : 0.567 9.235 14540 Z= 0.280 Chirality : 0.042 0.158 1726 Planarity : 0.004 0.031 1812 Dihedral : 4.215 21.695 1448 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.57 % Rotamer Outliers : 0.17 % 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: -0.13 (0.23), residues: 1346 helix: 1.36 (0.18), residues: 822 sheet: 2.79 (0.82), residues: 36 loop : -3.03 (0.25), residues: 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.606 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.1152 time to fit residues: 7.0700 Evaluate side-chains 30 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 115 optimal weight: 0.0870 chunk 34 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 overall best weight: 2.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10698 Z= 0.187 Angle : 0.568 8.514 14540 Z= 0.282 Chirality : 0.042 0.148 1726 Planarity : 0.003 0.032 1812 Dihedral : 4.123 21.819 1448 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.57 % 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: -0.01 (0.23), residues: 1346 helix: 1.40 (0.18), residues: 828 sheet: 3.02 (0.81), residues: 36 loop : -2.95 (0.25), residues: 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.569 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1257 time to fit residues: 7.0982 Evaluate side-chains 30 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 0.0050 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 10698 Z= 0.153 Angle : 0.562 8.077 14540 Z= 0.274 Chirality : 0.042 0.163 1726 Planarity : 0.003 0.031 1812 Dihedral : 4.002 21.519 1448 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.54 % Favored : 93.31 % 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: 0.10 (0.23), residues: 1346 helix: 1.40 (0.18), residues: 826 sheet: 3.47 (0.78), residues: 36 loop : -2.74 (0.26), residues: 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.586 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1397 time to fit residues: 8.3206 Evaluate side-chains 27 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.0770 chunk 25 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 129 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.0278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 10698 Z= 0.164 Angle : 0.569 7.913 14540 Z= 0.281 Chirality : 0.042 0.156 1726 Planarity : 0.004 0.058 1812 Dihedral : 4.056 21.971 1448 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.98 % Favored : 92.87 % 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: 0.20 (0.23), residues: 1346 helix: 1.49 (0.18), residues: 828 sheet: 3.50 (0.78), residues: 36 loop : -2.73 (0.25), residues: 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.633 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1481 time to fit residues: 8.6569 Evaluate side-chains 28 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 94 optimal weight: 0.2980 chunk 109 optimal weight: 7.9990 chunk 72 optimal weight: 0.0980 chunk 129 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.1938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 10698 Z= 0.157 Angle : 0.558 7.320 14540 Z= 0.271 Chirality : 0.041 0.159 1726 Planarity : 0.004 0.050 1812 Dihedral : 3.939 23.879 1448 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.98 % Favored : 92.72 % 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: -0.47 (0.22), residues: 1346 helix: 0.89 (0.18), residues: 828 sheet: 2.83 (0.78), residues: 36 loop : -2.84 (0.25), residues: 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.631 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1345 time to fit residues: 8.1998 Evaluate side-chains 28 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 chunk 87 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 0.0270 chunk 101 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 123 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 10698 Z= 0.149 Angle : 0.537 5.983 14540 Z= 0.258 Chirality : 0.041 0.157 1726 Planarity : 0.003 0.027 1812 Dihedral : 3.792 22.250 1448 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.13 % Favored : 92.57 % 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: -0.45 (0.22), residues: 1346 helix: 0.90 (0.18), residues: 832 sheet: 2.66 (0.78), residues: 36 loop : -2.81 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.609 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1204 time to fit residues: 7.8337 Evaluate side-chains 27 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 10698 Z= 0.153 Angle : 0.559 6.958 14540 Z= 0.267 Chirality : 0.042 0.167 1726 Planarity : 0.003 0.026 1812 Dihedral : 3.703 19.673 1448 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.43 % Favored : 92.27 % 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: -0.54 (0.22), residues: 1346 helix: 0.81 (0.18), residues: 832 sheet: 2.49 (0.75), residues: 36 loop : -2.80 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.668 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1523 time to fit residues: 9.8588 Evaluate side-chains 29 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 122 optimal weight: 0.9980 chunk 106 optimal weight: 0.0030 chunk 11 optimal weight: 9.9990 chunk 82 optimal weight: 0.0470 chunk 65 optimal weight: 0.0070 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 overall best weight: 0.1106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 10698 Z= 0.155 Angle : 0.563 8.766 14540 Z= 0.267 Chirality : 0.042 0.167 1726 Planarity : 0.003 0.027 1812 Dihedral : 3.705 18.311 1448 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.43 % Favored : 92.27 % 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: -0.64 (0.22), residues: 1346 helix: 0.78 (0.18), residues: 834 sheet: 0.79 (0.72), residues: 50 loop : -2.92 (0.25), residues: 462 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.574 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1319 time to fit residues: 8.6848 Evaluate side-chains 29 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 44 optimal weight: 0.0170 chunk 109 optimal weight: 0.0020 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 0.0060 chunk 93 optimal weight: 0.0000 chunk 6 optimal weight: 0.0060 overall best weight: 0.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.055107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.044171 restraints weight = 43851.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045241 restraints weight = 27762.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045991 restraints weight = 19763.386| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 10698 Z= 0.148 Angle : 0.557 7.001 14540 Z= 0.264 Chirality : 0.042 0.187 1726 Planarity : 0.003 0.026 1812 Dihedral : 3.671 17.304 1448 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.43 % Favored : 92.27 % 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: -0.77 (0.22), residues: 1346 helix: 0.63 (0.17), residues: 836 sheet: 0.88 (0.73), residues: 50 loop : -2.89 (0.25), residues: 460 =============================================================================== Job complete usr+sys time: 1590.05 seconds wall clock time: 30 minutes 20.71 seconds (1820.71 seconds total)