Starting phenix.real_space_refine on Thu Mar 14 19:40:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/03_2024/7rra_24657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/03_2024/7rra_24657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/03_2024/7rra_24657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/03_2024/7rra_24657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/03_2024/7rra_24657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/03_2024/7rra_24657.pdb" } resolution = 4.4 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= 0.004 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 44 5.16 5 C 6164 2.51 5 N 1686 2.21 5 O 1714 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: 9608 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4804 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Chain: "A" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4804 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Time building chain proxies: 5.26, per 1000 atoms: 0.55 Number of scatterers: 9608 At special positions: 0 Unit cell: (112.77, 80.55, 144.99, 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 44 16.00 O 1714 8.00 N 1686 7.00 C 6164 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: 4.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 66.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 68 through 82 Processing helix chain 'A' and resid 89 through 124 Processing helix chain 'A' and resid 127 through 174 removed outlier: 4.565A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 193 through 236 removed outlier: 4.260A pdb=" N ASP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 4.201A pdb=" N ASP A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 5.177A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 288 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 299 through 339 removed outlier: 3.985A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 330 " --> pdb=" O TRP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 356 Proline residue: A 350 - end of helix removed outlier: 4.114A pdb=" N THR A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 4.799A pdb=" N ALA A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 442 removed outlier: 4.841A pdb=" N LYS A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLU A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 586 through 592 Processing helix chain 'A' and resid 607 through 621 removed outlier: 4.148A pdb=" N LYS A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.906A pdb=" N TYR A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 82 Processing helix chain 'B' and resid 89 through 124 Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 142 through 175 Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 199 through 236 Proline residue: B 218 - end of helix removed outlier: 4.202A pdb=" N ASP B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 265 through 288 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 299 through 355 removed outlier: 3.908A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 330 " --> pdb=" O TRP B 326 " (cutoff:3.500A) Proline residue: B 350 - end of helix removed outlier: 4.114A pdb=" N THR B 353 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 374 through 442 removed outlier: 4.841A pdb=" N LYS B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 563 through 567 Processing helix chain 'B' and resid 573 through 583 Processing helix chain 'B' and resid 585 through 592 Processing helix chain 'B' and resid 608 through 621 Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.906A pdb=" N TYR B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 466 through 469 removed outlier: 3.787A pdb=" N ILE A 475 " --> pdb=" O TYR A 532 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 679 through 683 removed outlier: 7.458A pdb=" N LEU A 654 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ILE A 505 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER A 656 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N GLY A 507 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 466 through 469 removed outlier: 3.787A pdb=" N ILE B 475 " --> pdb=" O TYR B 532 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 503 through 507 removed outlier: 6.537A pdb=" N HIS B 669 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N THR B 506 " --> pdb=" O HIS B 669 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 671 " --> pdb=" O THR B 506 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 623 hydrogen bonds defined for protein. 1746 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: 2.54 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3146 1.34 - 1.46: 2073 1.46 - 1.58: 4525 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9818 Sorted by residual: bond pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.62e+00 bond pdb=" N GLU A 498 " pdb=" CA GLU A 498 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.05e+00 bond pdb=" N MET B 539 " pdb=" CA MET B 539 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.29e+00 bond pdb=" N GLU B 498 " pdb=" CA GLU B 498 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.37e-02 5.33e+03 7.25e+00 bond pdb=" N MET B 501 " pdb=" CA MET B 501 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.14e+00 ... (remaining 9813 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 269 107.16 - 113.88: 5483 113.88 - 120.60: 4177 120.60 - 127.32: 3253 127.32 - 134.03: 112 Bond angle restraints: 13294 Sorted by residual: angle pdb=" N GLN A 611 " pdb=" CA GLN A 611 " pdb=" C GLN A 611 " ideal model delta sigma weight residual 111.71 107.53 4.18 1.15e+00 7.56e-01 1.32e+01 angle pdb=" N GLN B 611 " pdb=" CA GLN B 611 " pdb=" C GLN B 611 " ideal model delta sigma weight residual 111.71 107.57 4.14 1.15e+00 7.56e-01 1.30e+01 angle pdb=" CA GLU B 498 " pdb=" C GLU B 498 " pdb=" O GLU B 498 " ideal model delta sigma weight residual 121.99 118.13 3.86 1.14e+00 7.69e-01 1.14e+01 angle pdb=" CA GLN B 472 " pdb=" C GLN B 472 " pdb=" O GLN B 472 " ideal model delta sigma weight residual 122.03 117.84 4.19 1.25e+00 6.40e-01 1.13e+01 angle pdb=" CA GLN A 472 " pdb=" C GLN A 472 " pdb=" O GLN A 472 " ideal model delta sigma weight residual 122.03 117.86 4.17 1.25e+00 6.40e-01 1.11e+01 ... (remaining 13289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 5211 16.04 - 32.08: 491 32.08 - 48.12: 159 48.12 - 64.16: 12 64.16 - 80.20: 9 Dihedral angle restraints: 5882 sinusoidal: 2376 harmonic: 3506 Sorted by residual: dihedral pdb=" CA ARG B 69 " pdb=" CB ARG B 69 " pdb=" CG ARG B 69 " pdb=" CD ARG B 69 " ideal model delta sinusoidal sigma weight residual -60.00 -113.42 53.42 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA ARG A 69 " pdb=" CB ARG A 69 " pdb=" CG ARG A 69 " pdb=" CD ARG A 69 " ideal model delta sinusoidal sigma weight residual -60.00 -113.37 53.37 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA TYR B 406 " pdb=" C TYR B 406 " pdb=" N LYS B 407 " pdb=" CA LYS B 407 " ideal model delta harmonic sigma weight residual 180.00 -165.18 -14.82 0 5.00e+00 4.00e-02 8.78e+00 ... (remaining 5879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1191 0.047 - 0.095: 228 0.095 - 0.142: 58 0.142 - 0.190: 5 0.190 - 0.237: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CA LEU B 325 " pdb=" N LEU B 325 " pdb=" C LEU B 325 " pdb=" CB LEU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA HIS A 283 " pdb=" N HIS A 283 " pdb=" C HIS A 283 " pdb=" CB HIS A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA VAL B 183 " pdb=" N VAL B 183 " pdb=" C VAL B 183 " pdb=" CB VAL B 183 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 1481 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 618 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C MET A 618 " -0.033 2.00e-02 2.50e+03 pdb=" O MET A 618 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 619 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 618 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C MET B 618 " -0.033 2.00e-02 2.50e+03 pdb=" O MET B 618 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE B 619 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 349 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 350 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " -0.021 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2033 2.79 - 3.32: 10073 3.32 - 3.84: 15830 3.84 - 4.37: 17559 4.37 - 4.90: 29272 Nonbonded interactions: 74767 Sorted by model distance: nonbonded pdb=" O GLU A 376 " pdb=" OG SER A 379 " model vdw 2.261 2.440 nonbonded pdb=" O GLU B 376 " pdb=" OG SER B 379 " model vdw 2.261 2.440 nonbonded pdb=" OE2 GLU B 272 " pdb=" NE2 GLN B 316 " model vdw 2.314 2.520 nonbonded pdb=" OE2 GLU A 272 " pdb=" NE2 GLN A 316 " model vdw 2.314 2.520 nonbonded pdb=" NH2 ARG B 280 " pdb=" OE1 GLN A 195 " model vdw 2.327 2.520 ... (remaining 74762 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 No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.680 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.430 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 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 : 0.003 0.042 9818 Z= 0.196 Angle : 0.593 7.776 13294 Z= 0.338 Chirality : 0.040 0.237 1484 Planarity : 0.003 0.037 1688 Dihedral : 13.752 80.198 3626 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 1.98 (0.24), residues: 1196 helix: 2.17 (0.18), residues: 816 sheet: 1.98 (0.48), residues: 88 loop : -1.51 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 601 HIS 0.003 0.001 HIS A 283 PHE 0.007 0.001 PHE A 385 TYR 0.020 0.001 TYR A 171 ARG 0.003 0.000 ARG B 538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 428 ASP cc_start: 0.7080 (t0) cc_final: 0.6569 (t70) REVERT: B 501 MET cc_start: 0.5014 (ppp) cc_final: 0.3868 (ppp) REVERT: A 428 ASP cc_start: 0.7418 (t0) cc_final: 0.7054 (t0) REVERT: A 501 MET cc_start: 0.6363 (ppp) cc_final: 0.5200 (ppp) REVERT: A 674 ASP cc_start: 0.6859 (p0) cc_final: 0.6351 (p0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2764 time to fit residues: 37.7855 Evaluate side-chains 72 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9818 Z= 0.256 Angle : 0.650 7.629 13294 Z= 0.341 Chirality : 0.041 0.259 1484 Planarity : 0.005 0.028 1688 Dihedral : 4.259 20.128 1344 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.10 % Allowed : 7.10 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1196 helix: 1.75 (0.17), residues: 796 sheet: 1.97 (0.47), residues: 88 loop : -1.27 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 595 HIS 0.007 0.002 HIS B 283 PHE 0.014 0.002 PHE A 175 TYR 0.026 0.002 TYR B 171 ARG 0.007 0.001 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 PHE cc_start: 0.7524 (t80) cc_final: 0.6370 (t80) REVERT: B 186 MET cc_start: 0.6568 (tmm) cc_final: 0.6251 (tmm) REVERT: B 428 ASP cc_start: 0.8123 (t0) cc_final: 0.7505 (t70) REVERT: B 501 MET cc_start: 0.5611 (ppp) cc_final: 0.4633 (ppp) REVERT: B 539 MET cc_start: 0.9030 (mpp) cc_final: 0.8794 (mpp) REVERT: A 146 PHE cc_start: 0.7326 (t80) cc_final: 0.6217 (t80) REVERT: A 186 MET cc_start: 0.6316 (tmm) cc_final: 0.6100 (tmm) REVERT: A 428 ASP cc_start: 0.7712 (t0) cc_final: 0.7390 (t0) REVERT: A 501 MET cc_start: 0.6705 (ppp) cc_final: 0.5822 (ppp) outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.2613 time to fit residues: 34.3112 Evaluate side-chains 74 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9818 Z= 0.167 Angle : 0.528 9.505 13294 Z= 0.271 Chirality : 0.038 0.133 1484 Planarity : 0.004 0.057 1688 Dihedral : 4.097 18.117 1344 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 1.72 (0.24), residues: 1196 helix: 1.95 (0.18), residues: 802 sheet: 1.99 (0.47), residues: 88 loop : -1.39 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.003 0.001 HIS A 169 PHE 0.009 0.001 PHE B 517 TYR 0.027 0.001 TYR B 171 ARG 0.005 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 PHE cc_start: 0.7341 (t80) cc_final: 0.6126 (t80) REVERT: B 186 MET cc_start: 0.6650 (tmm) cc_final: 0.6346 (tmm) REVERT: B 428 ASP cc_start: 0.7989 (t0) cc_final: 0.7429 (t70) REVERT: B 501 MET cc_start: 0.5669 (ppp) cc_final: 0.4612 (ppp) REVERT: B 539 MET cc_start: 0.8987 (mpp) cc_final: 0.8755 (mpp) REVERT: A 146 PHE cc_start: 0.7155 (t80) cc_final: 0.6209 (t80) REVERT: A 172 ARG cc_start: 0.6970 (mmp-170) cc_final: 0.6663 (mmp-170) REVERT: A 186 MET cc_start: 0.6411 (tmm) cc_final: 0.6096 (tmm) REVERT: A 428 ASP cc_start: 0.7490 (t0) cc_final: 0.7209 (t0) REVERT: A 501 MET cc_start: 0.6699 (ppp) cc_final: 0.5712 (ppp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2352 time to fit residues: 31.6016 Evaluate side-chains 72 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 HIS ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9818 Z= 0.185 Angle : 0.543 10.564 13294 Z= 0.281 Chirality : 0.038 0.143 1484 Planarity : 0.004 0.045 1688 Dihedral : 4.155 19.188 1344 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 1.60 (0.24), residues: 1196 helix: 1.86 (0.18), residues: 814 sheet: 1.89 (0.47), residues: 88 loop : -1.58 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.004 0.001 HIS B 283 PHE 0.010 0.001 PHE A 175 TYR 0.025 0.001 TYR B 171 ARG 0.006 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 PHE cc_start: 0.7502 (t80) cc_final: 0.6339 (t80) REVERT: B 186 MET cc_start: 0.6779 (tmm) cc_final: 0.6475 (tmm) REVERT: B 422 MET cc_start: 0.6036 (tmm) cc_final: 0.5833 (tmm) REVERT: B 428 ASP cc_start: 0.8024 (t0) cc_final: 0.7478 (t70) REVERT: B 501 MET cc_start: 0.6012 (ppp) cc_final: 0.4902 (ppp) REVERT: B 539 MET cc_start: 0.9013 (mpp) cc_final: 0.8781 (mpp) REVERT: A 146 PHE cc_start: 0.7329 (t80) cc_final: 0.6270 (t80) REVERT: A 186 MET cc_start: 0.6702 (tmm) cc_final: 0.6378 (tmm) REVERT: A 428 ASP cc_start: 0.7445 (t0) cc_final: 0.7182 (t0) REVERT: A 501 MET cc_start: 0.6779 (ppp) cc_final: 0.5682 (ppp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2050 time to fit residues: 26.6916 Evaluate side-chains 70 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 0.0270 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9818 Z= 0.214 Angle : 0.579 10.992 13294 Z= 0.303 Chirality : 0.039 0.198 1484 Planarity : 0.004 0.041 1688 Dihedral : 4.293 19.983 1344 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 1.46 (0.24), residues: 1196 helix: 1.76 (0.18), residues: 808 sheet: 1.85 (0.49), residues: 88 loop : -1.54 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 339 HIS 0.005 0.001 HIS B 283 PHE 0.029 0.002 PHE B 130 TYR 0.030 0.002 TYR B 171 ARG 0.005 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: B 146 PHE cc_start: 0.7371 (t80) cc_final: 0.6420 (t80) REVERT: B 186 MET cc_start: 0.6851 (tmm) cc_final: 0.6425 (tmm) REVERT: B 325 LEU cc_start: 0.7653 (mp) cc_final: 0.7295 (mp) REVERT: B 422 MET cc_start: 0.6081 (tmm) cc_final: 0.5857 (tmm) REVERT: B 428 ASP cc_start: 0.8079 (t0) cc_final: 0.7531 (t70) REVERT: B 501 MET cc_start: 0.6479 (ppp) cc_final: 0.5410 (ppp) REVERT: A 122 ILE cc_start: 0.7163 (mm) cc_final: 0.6934 (mt) REVERT: A 146 PHE cc_start: 0.7251 (t80) cc_final: 0.6366 (t80) REVERT: A 428 ASP cc_start: 0.7428 (t0) cc_final: 0.7201 (t0) REVERT: A 501 MET cc_start: 0.7127 (ppp) cc_final: 0.5992 (ppp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2348 time to fit residues: 29.8899 Evaluate side-chains 71 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9818 Z= 0.230 Angle : 0.606 9.506 13294 Z= 0.317 Chirality : 0.040 0.200 1484 Planarity : 0.004 0.039 1688 Dihedral : 4.398 20.526 1344 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 1.32 (0.24), residues: 1196 helix: 1.60 (0.18), residues: 810 sheet: 1.72 (0.49), residues: 88 loop : -1.42 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 339 HIS 0.005 0.001 HIS B 283 PHE 0.029 0.002 PHE A 130 TYR 0.035 0.002 TYR B 171 ARG 0.013 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: B 146 PHE cc_start: 0.7421 (t80) cc_final: 0.6427 (t80) REVERT: B 186 MET cc_start: 0.6940 (tmm) cc_final: 0.6684 (tmm) REVERT: B 325 LEU cc_start: 0.7676 (mp) cc_final: 0.7302 (mp) REVERT: B 428 ASP cc_start: 0.8092 (t0) cc_final: 0.7612 (t70) REVERT: B 501 MET cc_start: 0.6661 (ppp) cc_final: 0.5559 (ppp) REVERT: A 146 PHE cc_start: 0.7262 (t80) cc_final: 0.6377 (t80) REVERT: A 428 ASP cc_start: 0.7686 (t0) cc_final: 0.7371 (t0) REVERT: A 501 MET cc_start: 0.6256 (ppp) cc_final: 0.5260 (ppp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2322 time to fit residues: 30.6539 Evaluate side-chains 75 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9818 Z= 0.371 Angle : 0.805 11.682 13294 Z= 0.432 Chirality : 0.047 0.280 1484 Planarity : 0.006 0.065 1688 Dihedral : 5.119 21.445 1344 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 28.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 1196 helix: 0.62 (0.17), residues: 804 sheet: 1.08 (0.51), residues: 88 loop : -1.85 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 77 HIS 0.010 0.002 HIS A 587 PHE 0.026 0.004 PHE B 175 TYR 0.054 0.003 TYR A 171 ARG 0.011 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.965 Fit side-chains REVERT: B 186 MET cc_start: 0.7112 (tmm) cc_final: 0.6814 (tmm) REVERT: B 325 LEU cc_start: 0.7873 (mp) cc_final: 0.7650 (mp) REVERT: B 428 ASP cc_start: 0.7867 (t0) cc_final: 0.7403 (t0) REVERT: B 501 MET cc_start: 0.7380 (ppp) cc_final: 0.6929 (ppp) REVERT: B 602 LYS cc_start: 0.6666 (mmtt) cc_final: 0.6081 (mmtt) REVERT: A 146 PHE cc_start: 0.7363 (t80) cc_final: 0.6293 (t80) REVERT: A 428 ASP cc_start: 0.8096 (t0) cc_final: 0.7844 (t0) REVERT: A 501 MET cc_start: 0.5997 (ppp) cc_final: 0.5624 (ppp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2220 time to fit residues: 26.8893 Evaluate side-chains 69 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 GLN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9818 Z= 0.183 Angle : 0.615 11.156 13294 Z= 0.316 Chirality : 0.040 0.146 1484 Planarity : 0.004 0.039 1688 Dihedral : 4.629 22.148 1344 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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 (0.24), residues: 1196 helix: 1.37 (0.17), residues: 806 sheet: 1.23 (0.50), residues: 88 loop : -1.57 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 77 HIS 0.003 0.001 HIS B 502 PHE 0.019 0.002 PHE B 83 TYR 0.032 0.002 TYR A 171 ARG 0.004 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.046 Fit side-chains REVERT: B 115 ASP cc_start: 0.4181 (m-30) cc_final: 0.3963 (m-30) REVERT: B 186 MET cc_start: 0.7107 (tmm) cc_final: 0.6799 (tmm) REVERT: B 325 LEU cc_start: 0.7641 (mp) cc_final: 0.7246 (mp) REVERT: B 329 MET cc_start: 0.5262 (mmp) cc_final: 0.5024 (mmp) REVERT: B 428 ASP cc_start: 0.7695 (t0) cc_final: 0.7332 (t0) REVERT: B 501 MET cc_start: 0.7139 (ppp) cc_final: 0.6320 (ppp) REVERT: A 130 PHE cc_start: 0.7473 (m-10) cc_final: 0.6921 (m-10) REVERT: A 146 PHE cc_start: 0.7277 (t80) cc_final: 0.6402 (t80) REVERT: A 329 MET cc_start: 0.5596 (mmp) cc_final: 0.5139 (mmp) REVERT: A 428 ASP cc_start: 0.7804 (t0) cc_final: 0.7319 (t0) REVERT: A 501 MET cc_start: 0.6336 (ppp) cc_final: 0.5873 (ppp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2091 time to fit residues: 27.0177 Evaluate side-chains 72 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9818 Z= 0.219 Angle : 0.626 10.984 13294 Z= 0.327 Chirality : 0.040 0.184 1484 Planarity : 0.004 0.040 1688 Dihedral : 4.696 21.286 1344 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 0.83 (0.23), residues: 1196 helix: 1.33 (0.17), residues: 800 sheet: 1.09 (0.51), residues: 88 loop : -1.67 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 77 HIS 0.005 0.001 HIS A 283 PHE 0.013 0.002 PHE A 71 TYR 0.031 0.002 TYR A 171 ARG 0.005 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.115 Fit side-chains REVERT: B 186 MET cc_start: 0.7012 (tmm) cc_final: 0.6742 (tmm) REVERT: B 325 LEU cc_start: 0.7731 (mp) cc_final: 0.7324 (mp) REVERT: B 428 ASP cc_start: 0.7691 (t0) cc_final: 0.7290 (t0) REVERT: B 501 MET cc_start: 0.6398 (ppp) cc_final: 0.5646 (ppp) REVERT: A 115 ASP cc_start: 0.3563 (m-30) cc_final: 0.3356 (m-30) REVERT: A 146 PHE cc_start: 0.7380 (t80) cc_final: 0.6409 (t80) REVERT: A 428 ASP cc_start: 0.7835 (t0) cc_final: 0.7357 (t0) REVERT: A 501 MET cc_start: 0.5811 (ppp) cc_final: 0.5521 (ppp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2209 time to fit residues: 26.6551 Evaluate side-chains 71 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0040 chunk 79 optimal weight: 0.0270 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 overall best weight: 1.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9818 Z= 0.188 Angle : 0.612 10.652 13294 Z= 0.313 Chirality : 0.040 0.198 1484 Planarity : 0.004 0.040 1688 Dihedral : 4.612 21.712 1344 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 1.01 (0.24), residues: 1196 helix: 1.49 (0.18), residues: 798 sheet: 1.08 (0.51), residues: 88 loop : -1.63 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 77 HIS 0.003 0.001 HIS A 283 PHE 0.012 0.001 PHE B 83 TYR 0.031 0.002 TYR A 171 ARG 0.004 0.000 ARG B 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.111 Fit side-chains REVERT: B 186 MET cc_start: 0.6999 (tmm) cc_final: 0.6724 (tmm) REVERT: B 325 LEU cc_start: 0.7830 (mp) cc_final: 0.7553 (mp) REVERT: B 346 MET cc_start: 0.7494 (mmp) cc_final: 0.6735 (mmp) REVERT: B 428 ASP cc_start: 0.7586 (t0) cc_final: 0.7233 (t0) REVERT: B 501 MET cc_start: 0.6339 (ppp) cc_final: 0.5587 (ppp) REVERT: A 130 PHE cc_start: 0.5940 (m-10) cc_final: 0.5459 (m-10) REVERT: A 146 PHE cc_start: 0.7368 (t80) cc_final: 0.6583 (t80) REVERT: A 346 MET cc_start: 0.7387 (mmp) cc_final: 0.7064 (mmp) REVERT: A 428 ASP cc_start: 0.7770 (t0) cc_final: 0.7304 (t0) REVERT: A 501 MET cc_start: 0.5765 (ppp) cc_final: 0.5496 (ppp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2164 time to fit residues: 26.4420 Evaluate side-chains 70 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.0040 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.094157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.084958 restraints weight = 71353.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.086762 restraints weight = 43339.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.087972 restraints weight = 29402.587| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9818 Z= 0.164 Angle : 0.584 10.170 13294 Z= 0.295 Chirality : 0.040 0.148 1484 Planarity : 0.004 0.038 1688 Dihedral : 4.425 20.182 1344 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.41 (0.24), residues: 1196 helix: 1.85 (0.18), residues: 804 sheet: 1.06 (0.51), residues: 88 loop : -1.65 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 77 HIS 0.003 0.001 HIS A 584 PHE 0.012 0.001 PHE B 130 TYR 0.023 0.002 TYR A 171 ARG 0.003 0.000 ARG A 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.86 seconds wall clock time: 30 minutes 48.30 seconds (1848.30 seconds total)