Starting phenix.real_space_refine on Sat Dec 9 00:53:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/12_2023/7rra_24657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/12_2023/7rra_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_24657/12_2023/7rra_24657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/12_2023/7rra_24657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/12_2023/7rra_24657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rra_24657/12_2023/7rra_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-1.21rc1-5172/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: 5.35, per 1000 atoms: 0.56 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: 3.83 Conformation dependent library (CDL) restraints added in 1.8 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: 0.89 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: 2.47 Time building geometry restraints manager: 4.06 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.840 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.760 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- 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 : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2798 time to fit residues: 38.1568 Evaluate side-chains 70 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5398 ------------------------------------------------------------------------------- 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: 7.9990 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: 5.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.6010 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9818 Z= 0.281 Angle : 0.648 8.611 13294 Z= 0.340 Chirality : 0.041 0.287 1484 Planarity : 0.005 0.028 1688 Dihedral : 4.201 18.183 1344 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1196 helix: 1.77 (0.18), residues: 796 sheet: 1.93 (0.46), residues: 88 loop : -1.30 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 339 HIS 0.008 0.002 HIS A 283 PHE 0.014 0.002 PHE B 71 TYR 0.025 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 94 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2724 time to fit residues: 35.0258 Evaluate side-chains 68 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5207 ------------------------------------------------------------------------------- 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: 9.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 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: 0.6051 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9818 Z= 0.238 Angle : 0.589 9.525 13294 Z= 0.308 Chirality : 0.040 0.180 1484 Planarity : 0.005 0.053 1688 Dihedral : 4.269 19.230 1344 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: 1.33 (0.24), residues: 1196 helix: 1.63 (0.18), residues: 806 sheet: 1.88 (0.47), residues: 88 loop : -1.51 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 339 HIS 0.004 0.001 HIS A 283 PHE 0.022 0.002 PHE B 146 TYR 0.033 0.002 TYR B 171 ARG 0.006 0.001 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 88 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2467 time to fit residues: 30.0525 Evaluate side-chains 67 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5406 ------------------------------------------------------------------------------- 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: 1.9990 chunk 82 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.5985 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9818 Z= 0.167 Angle : 0.540 10.790 13294 Z= 0.278 Chirality : 0.038 0.134 1484 Planarity : 0.004 0.062 1688 Dihedral : 4.185 19.764 1344 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 1.55 (0.24), residues: 1196 helix: 1.83 (0.18), residues: 814 sheet: 1.89 (0.48), residues: 88 loop : -1.60 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS A 97 PHE 0.014 0.001 PHE A 146 TYR 0.027 0.001 TYR B 171 ARG 0.008 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 90 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2579 time to fit residues: 33.0213 Evaluate side-chains 68 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5787 ------------------------------------------------------------------------------- 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: 7.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 0.0170 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9818 Z= 0.298 Angle : 0.674 10.527 13294 Z= 0.359 Chirality : 0.041 0.184 1484 Planarity : 0.005 0.054 1688 Dihedral : 4.612 20.053 1344 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: 0.93 (0.24), residues: 1196 helix: 1.31 (0.18), residues: 810 sheet: 1.74 (0.51), residues: 88 loop : -1.68 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 339 HIS 0.008 0.002 HIS B 283 PHE 0.026 0.003 PHE A 130 TYR 0.037 0.002 TYR B 171 ARG 0.011 0.001 ARG A 120 *********************** 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 87 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.251 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2363 time to fit residues: 29.2452 Evaluate side-chains 66 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6115 ------------------------------------------------------------------------------- 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: 4.9990 chunk 104 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** ** 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: 0.6069 moved from start: 0.3306 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= 0.193 Angle : 0.597 11.245 13294 Z= 0.310 Chirality : 0.040 0.192 1484 Planarity : 0.004 0.042 1688 Dihedral : 4.481 21.033 1344 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 1.21 (0.24), residues: 1196 helix: 1.53 (0.18), residues: 812 sheet: 1.80 (0.51), residues: 88 loop : -1.56 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 339 HIS 0.004 0.001 HIS B 587 PHE 0.018 0.002 PHE B 130 TYR 0.033 0.002 TYR A 171 ARG 0.005 0.000 ARG B 172 *********************** 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 90 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2302 time to fit residues: 29.7786 Evaluate side-chains 69 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4617 ------------------------------------------------------------------------------- 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: 9.9990 chunk 13 optimal weight: 9.9990 chunk 66 optimal weight: 0.0770 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.9744 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9818 Z= 0.302 Angle : 0.716 11.617 13294 Z= 0.378 Chirality : 0.043 0.276 1484 Planarity : 0.005 0.047 1688 Dihedral : 4.850 21.320 1344 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 0.51 (0.23), residues: 1196 helix: 1.00 (0.18), residues: 804 sheet: 1.50 (0.52), residues: 88 loop : -1.76 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 339 HIS 0.008 0.002 HIS A 587 PHE 0.018 0.003 PHE B 175 TYR 0.042 0.003 TYR A 171 ARG 0.009 0.001 ARG B 172 *********************** 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 84 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.112 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2325 time to fit residues: 27.7845 Evaluate side-chains 67 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4230 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 0.0050 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 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 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: 0.6030 moved from start: 0.3686 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= 0.180 Angle : 0.608 11.906 13294 Z= 0.309 Chirality : 0.040 0.149 1484 Planarity : 0.004 0.039 1688 Dihedral : 4.482 21.689 1344 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 1.28 (0.24), residues: 1196 helix: 1.62 (0.18), residues: 802 sheet: 1.54 (0.51), residues: 88 loop : -1.46 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 77 HIS 0.003 0.001 HIS A 210 PHE 0.017 0.002 PHE B 83 TYR 0.026 0.002 TYR A 171 ARG 0.004 0.000 ARG A 401 *********************** 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 92 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.052 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2509 time to fit residues: 32.2378 Evaluate side-chains 75 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5339 ------------------------------------------------------------------------------- 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: 0.2980 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 0.0030 chunk 84 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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: 0.5995 moved from start: 0.3589 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= 0.168 Angle : 0.608 12.038 13294 Z= 0.305 Chirality : 0.040 0.152 1484 Planarity : 0.004 0.040 1688 Dihedral : 4.430 20.885 1344 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.44 (0.24), residues: 1196 helix: 1.80 (0.18), residues: 804 sheet: 1.53 (0.51), residues: 88 loop : -1.58 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 595 HIS 0.003 0.001 HIS A 210 PHE 0.013 0.001 PHE A 130 TYR 0.022 0.002 TYR A 171 ARG 0.006 0.000 ARG B 591 *********************** 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 89 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.157 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2405 time to fit residues: 30.4139 Evaluate side-chains 71 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7347 ------------------------------------------------------------------------------- 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: 0.0010 chunk 79 optimal weight: 0.0570 chunk 119 optimal weight: 0.0010 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.3479 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= 0.165 Angle : 0.604 13.197 13294 Z= 0.300 Chirality : 0.040 0.174 1484 Planarity : 0.004 0.040 1688 Dihedral : 4.386 20.267 1344 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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: 1.65 (0.25), residues: 1196 helix: 1.91 (0.18), residues: 810 sheet: 1.59 (0.52), residues: 88 loop : -1.42 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 326 HIS 0.003 0.001 HIS A 210 PHE 0.015 0.001 PHE B 130 TYR 0.020 0.002 TYR A 171 ARG 0.006 0.000 ARG B 104 ********************** 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 90 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.244 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2592 time to fit residues: 32.1440 Evaluate side-chains 72 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4469 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 0.0000 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.094251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.085248 restraints weight = 71762.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.087044 restraints weight = 43500.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.088246 restraints weight = 29358.523| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.3528 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= 0.172 Angle : 0.595 10.903 13294 Z= 0.299 Chirality : 0.040 0.187 1484 Planarity : 0.004 0.040 1688 Dihedral : 4.332 19.691 1344 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 1.59 (0.24), residues: 1196 helix: 1.90 (0.18), residues: 810 sheet: 1.60 (0.52), residues: 88 loop : -1.56 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 77 HIS 0.003 0.001 HIS A 210 PHE 0.012 0.001 PHE A 385 TYR 0.021 0.002 TYR A 171 ARG 0.004 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.51 seconds wall clock time: 32 minutes 23.22 seconds (1943.22 seconds total)