Starting phenix.real_space_refine on Fri Mar 15 02:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/03_2024/7s9d_24933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/03_2024/7s9d_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_24933/03_2024/7s9d_24933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/03_2024/7s9d_24933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/03_2024/7s9d_24933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9d_24933/03_2024/7s9d_24933.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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-dev-5265/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: 5.42, per 1000 atoms: 0.52 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: 4.64 Conformation dependent library (CDL) restraints added in 2.0 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: 1.07 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: 3.18 Time building geometry restraints manager: 4.95 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: 0.010 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.010 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.020 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.670 ------------------------------------------------------------------------------- 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 % Allowed : 0.96 % Favored : 98.70 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 472 HIS 0.016 0.003 HIS A 25 PHE 0.016 0.002 PHE A 213 TYR 0.013 0.002 TYR B 118 ARG 0.007 0.001 ARG B 281 *********************** 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 : 0.616 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.1605 time to fit residues: 7.4706 Evaluate side-chains 26 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.5980 ------------------------------------------------------------------------------- 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 447 ASN A 650 ASN A 689 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10698 Z= 0.182 Angle : 0.592 8.620 14540 Z= 0.297 Chirality : 0.044 0.192 1726 Planarity : 0.005 0.094 1812 Dihedral : 4.546 29.298 1448 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.73 % Favored : 92.12 % Rotamer: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.39 % 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: -0.36 (0.23), residues: 1346 helix: 1.18 (0.18), residues: 824 sheet: 2.52 (0.80), residues: 36 loop : -3.14 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.008 0.001 HIS A 25 PHE 0.015 0.001 PHE B 23 TYR 0.009 0.001 TYR A 118 ARG 0.004 0.000 ARG B 399 *********************** 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 37 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 575 MET cc_start: 0.9055 (mmt) cc_final: 0.8717 (mmp) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1222 time to fit residues: 7.0510 Evaluate side-chains 29 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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: 10.0000 chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 108 optimal weight: 0.0170 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 97 optimal weight: 0.7980 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10698 Z= 0.162 Angle : 0.561 9.129 14540 Z= 0.278 Chirality : 0.042 0.167 1726 Planarity : 0.004 0.046 1812 Dihedral : 4.241 20.827 1448 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.13 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: 1.35 (0.18), residues: 822 sheet: 3.01 (0.81), residues: 36 loop : -3.03 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 472 HIS 0.017 0.002 HIS B 25 PHE 0.015 0.001 PHE B 213 TYR 0.007 0.001 TYR B 118 ARG 0.004 0.000 ARG A 716 *********************** 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 38 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.9000 (mmp) cc_final: 0.8764 (mmp) REVERT: A 299 MET cc_start: 0.5866 (tpt) cc_final: 0.5517 (tpp) REVERT: A 357 MET cc_start: 0.8410 (tpt) cc_final: 0.7843 (tpp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1094 time to fit residues: 6.5911 Evaluate side-chains 30 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 0.0770 chunk 63 optimal weight: 0.0070 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 0.0000 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 115 optimal weight: 0.4980 chunk 34 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.3160 ------------------------------------------------------------------------------- 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** ** B 403 GLN ** 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: 0.7931 moved from start: 0.2108 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= 0.159 Angle : 0.572 8.379 14540 Z= 0.277 Chirality : 0.042 0.159 1726 Planarity : 0.003 0.036 1812 Dihedral : 4.081 21.947 1448 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.58 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -0.01 (0.23), residues: 1346 helix: 1.40 (0.18), residues: 824 sheet: 3.41 (0.80), residues: 36 loop : -2.94 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 472 HIS 0.011 0.002 HIS B 25 PHE 0.011 0.001 PHE A 391 TYR 0.010 0.001 TYR A 486 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 4 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 : 0.495 Fit side-chains REVERT: B 126 PHE cc_start: 0.8773 (m-80) cc_final: 0.8568 (m-80) REVERT: B 299 MET cc_start: 0.5983 (tpt) cc_final: 0.5632 (tpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1437 time to fit residues: 8.4456 Evaluate side-chains 30 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 0.0370 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 0.0050 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 overall best weight: 0.3272 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2354 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= 0.158 Angle : 0.543 7.054 14540 Z= 0.262 Chirality : 0.041 0.158 1726 Planarity : 0.003 0.027 1812 Dihedral : 3.883 16.918 1448 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.88 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: -0.50 (0.22), residues: 1346 helix: 0.91 (0.18), residues: 828 sheet: 3.11 (0.80), residues: 36 loop : -2.95 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 472 HIS 0.011 0.002 HIS B 220 PHE 0.019 0.001 PHE B 213 TYR 0.009 0.001 TYR B 501 ARG 0.010 0.000 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 5 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 : 0.637 Fit side-chains REVERT: B 126 PHE cc_start: 0.8830 (m-80) cc_final: 0.8584 (m-80) REVERT: B 225 MET cc_start: 0.8982 (mmp) cc_final: 0.8764 (mmp) REVERT: B 299 MET cc_start: 0.6041 (tpt) cc_final: 0.5690 (tpp) REVERT: B 453 MET cc_start: 0.6601 (mtt) cc_final: 0.5463 (mmt) REVERT: B 575 MET cc_start: 0.8977 (mmt) cc_final: 0.8474 (mmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1437 time to fit residues: 8.6985 Evaluate side-chains 31 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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: 0.0870 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 overall best weight: 1.3360 ------------------------------------------------------------------------------- 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: 0.7923 moved from start: 0.2416 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= 0.161 Angle : 0.551 6.647 14540 Z= 0.269 Chirality : 0.041 0.150 1726 Planarity : 0.003 0.030 1812 Dihedral : 3.913 22.390 1448 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.47 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.82 (0.18), residues: 828 sheet: 2.90 (0.80), residues: 36 loop : -3.04 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 462 HIS 0.010 0.001 HIS B 220 PHE 0.008 0.001 PHE B 391 TYR 0.009 0.001 TYR A 501 ARG 0.009 0.000 ARG A 502 *********************** 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 39 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 126 PHE cc_start: 0.8804 (m-80) cc_final: 0.8539 (m-80) REVERT: B 299 MET cc_start: 0.6054 (tpt) cc_final: 0.5687 (tpp) REVERT: B 357 MET cc_start: 0.8440 (tpt) cc_final: 0.7784 (tpp) REVERT: B 453 MET cc_start: 0.6661 (mtt) cc_final: 0.5525 (mmt) REVERT: B 575 MET cc_start: 0.8982 (mmt) cc_final: 0.8472 (mmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1208 time to fit residues: 7.3609 Evaluate side-chains 30 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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: 9.9990 chunk 73 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 80 optimal weight: 0.0170 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- 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: 0.7924 moved from start: 0.2451 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= 0.160 Angle : 0.537 6.771 14540 Z= 0.263 Chirality : 0.041 0.148 1726 Planarity : 0.003 0.026 1812 Dihedral : 3.865 21.089 1448 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.88 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.56 (0.22), residues: 1346 helix: 0.91 (0.18), residues: 828 sheet: 2.73 (0.80), residues: 36 loop : -3.05 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 472 HIS 0.009 0.001 HIS B 220 PHE 0.020 0.001 PHE A 213 TYR 0.005 0.001 TYR A 486 ARG 0.007 0.000 ARG A 502 *********************** 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 40 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.694 Fit side-chains REVERT: B 126 PHE cc_start: 0.8790 (m-80) cc_final: 0.8533 (m-80) REVERT: B 225 MET cc_start: 0.8973 (mmp) cc_final: 0.8756 (mmp) REVERT: B 299 MET cc_start: 0.5936 (tpt) cc_final: 0.5568 (tpp) REVERT: B 357 MET cc_start: 0.8634 (tpt) cc_final: 0.8004 (tpp) REVERT: B 453 MET cc_start: 0.6677 (mtt) cc_final: 0.6340 (mtp) REVERT: B 575 MET cc_start: 0.8986 (mmt) cc_final: 0.8506 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1238 time to fit residues: 7.7192 Evaluate side-chains 29 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 20.0000 chunk 25 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10698 Z= 0.169 Angle : 0.539 7.528 14540 Z= 0.262 Chirality : 0.041 0.148 1726 Planarity : 0.003 0.027 1812 Dihedral : 3.799 20.048 1448 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.62 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.52 (0.22), residues: 1346 helix: 0.96 (0.18), residues: 828 sheet: 2.43 (0.78), residues: 36 loop : -3.05 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 472 HIS 0.004 0.001 HIS B 25 PHE 0.009 0.001 PHE A 137 TYR 0.007 0.001 TYR A 501 ARG 0.003 0.000 ARG B 502 *********************** 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 41 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.629 Fit side-chains REVERT: B 126 PHE cc_start: 0.8800 (m-80) cc_final: 0.8536 (m-80) REVERT: B 299 MET cc_start: 0.5949 (tpt) cc_final: 0.5561 (tpp) REVERT: B 357 MET cc_start: 0.8694 (tpt) cc_final: 0.7965 (tpp) REVERT: B 575 MET cc_start: 0.8976 (mmt) cc_final: 0.8492 (mmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1237 time to fit residues: 7.9124 Evaluate side-chains 30 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 1.9990 chunk 123 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.0370 chunk 108 optimal weight: 0.0030 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 0.0980 chunk 79 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 overall best weight: 0.2068 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.2719 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= 0.151 Angle : 0.552 7.206 14540 Z= 0.264 Chirality : 0.041 0.156 1726 Planarity : 0.003 0.031 1812 Dihedral : 3.791 19.507 1448 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.88 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -0.65 (0.22), residues: 1346 helix: 0.81 (0.18), residues: 828 sheet: 2.23 (0.78), residues: 36 loop : -2.98 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 462 HIS 0.011 0.001 HIS B 220 PHE 0.018 0.001 PHE B 213 TYR 0.006 0.001 TYR B 546 ARG 0.003 0.000 ARG B 502 *********************** 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 40 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.579 Fit side-chains REVERT: B 126 PHE cc_start: 0.8800 (m-80) cc_final: 0.8536 (m-80) REVERT: B 299 MET cc_start: 0.6040 (tpt) cc_final: 0.5647 (tpp) REVERT: B 357 MET cc_start: 0.8512 (tpt) cc_final: 0.7958 (tpp) REVERT: B 453 MET cc_start: 0.6695 (mtt) cc_final: 0.5481 (mmt) REVERT: B 575 MET cc_start: 0.9007 (mmt) cc_final: 0.8565 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1368 time to fit residues: 8.2718 Evaluate side-chains 28 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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: 0.0170 chunk 60 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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: 0.7878 moved from start: 0.2925 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= 0.145 Angle : 0.548 7.100 14540 Z= 0.260 Chirality : 0.042 0.157 1726 Planarity : 0.003 0.030 1812 Dihedral : 3.708 19.036 1448 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.73 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.78 (0.22), residues: 1346 helix: 0.74 (0.18), residues: 838 sheet: 0.40 (0.72), residues: 50 loop : -3.12 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 472 HIS 0.004 0.001 HIS A 25 PHE 0.010 0.001 PHE A 351 TYR 0.006 0.001 TYR B 546 ARG 0.003 0.000 ARG A 502 ********************** 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 42 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.724 Fit side-chains REVERT: A 126 PHE cc_start: 0.8804 (m-80) cc_final: 0.8524 (m-80) REVERT: A 299 MET cc_start: 0.5943 (tpt) cc_final: 0.5589 (tpp) REVERT: A 357 MET cc_start: 0.8523 (tpt) cc_final: 0.7989 (tpp) REVERT: A 453 MET cc_start: 0.6718 (mtt) cc_final: 0.6287 (mtp) REVERT: A 575 MET cc_start: 0.9064 (mmt) cc_final: 0.8804 (mmp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1270 time to fit residues: 8.1437 Evaluate side-chains 29 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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: 6.9990 chunk 98 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.0570 chunk 44 optimal weight: 8.9990 chunk 109 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.0270 chunk 93 optimal weight: 0.0570 chunk 6 optimal weight: 0.4980 overall best weight: 0.1472 ------------------------------------------------------------------------------- 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** B 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.043705 restraints weight = 44141.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.044755 restraints weight = 27622.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.045514 restraints weight = 19603.758| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3151 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= 0.151 Angle : 0.571 8.430 14540 Z= 0.268 Chirality : 0.042 0.168 1726 Planarity : 0.003 0.027 1812 Dihedral : 3.705 18.465 1448 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.02 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.75 (0.22), residues: 1346 helix: 0.72 (0.18), residues: 838 sheet: 0.38 (0.72), residues: 50 loop : -3.01 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 462 HIS 0.003 0.001 HIS B 25 PHE 0.014 0.001 PHE A 213 TYR 0.007 0.001 TYR A 546 ARG 0.002 0.000 ARG B 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1633.79 seconds wall clock time: 30 minutes 40.16 seconds (1840.16 seconds total)