Starting phenix.real_space_refine on Sun Mar 10 19:02:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/03_2024/8ikj_35514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/03_2024/8ikj_35514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/03_2024/8ikj_35514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/03_2024/8ikj_35514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/03_2024/8ikj_35514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/03_2024/8ikj_35514.pdb" } resolution = 3.2 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= 0.013 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 28 5.16 5 C 2712 2.51 5 N 702 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4200 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 4158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 532, 4147 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 20, 'TRANS': 511} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 532, 4147 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 20, 'TRANS': 511} Chain breaks: 1 bond proxies already assigned to first conformer: 4226 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.78, per 1000 atoms: 1.14 Number of scatterers: 4200 At special positions: 0 Unit cell: (79.98, 92.07, 119.97, 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 28 16.00 O 758 8.00 N 702 7.00 C 2712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 495 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 513 " - pdb=" SG CYS R 527 " distance=2.03 Simple disulfide: pdb=" SG CYS R 612 " - pdb=" SG CYS R 684 " distance=2.03 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 Links applied NAG-ASN " NAG R 901 " - " ASN R 413 " " NAG R 902 " - " ASN R 406 " " NAG R 903 " - " ASN R 520 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 52.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'R' and resid 272 through 289 Processing helix chain 'R' and resid 293 through 311 Processing helix chain 'R' and resid 319 through 343 removed outlier: 3.814A pdb=" N LYS R 343 " --> pdb=" O ARG R 339 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 390 removed outlier: 3.531A pdb=" N ALA R 389 " --> pdb=" O TRP R 385 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY R 390 " --> pdb=" O ALA R 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 385 through 390' Processing helix chain 'R' and resid 406 through 410 Processing helix chain 'R' and resid 419 through 431 Processing helix chain 'R' and resid 548 through 572 Processing helix chain 'R' and resid 577 through 601 Processing helix chain 'R' and resid 609 through 643 Processing helix chain 'R' and resid 651 through 674 Proline residue: R 663 - end of helix Processing helix chain 'R' and resid 691 through 719 removed outlier: 3.675A pdb=" N SER R 695 " --> pdb=" O GLY R 691 " (cutoff:3.500A) Proline residue: R 699 - end of helix Processing helix chain 'R' and resid 735 through 756 Processing helix chain 'R' and resid 766 through 787 removed outlier: 3.610A pdb=" N VAL R 770 " --> pdb=" O VAL R 766 " (cutoff:3.500A) Processing helix chain 'R' and resid 790 through 801 removed outlier: 3.572A pdb=" N ARG R 794 " --> pdb=" O ASN R 790 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 348 through 353 removed outlier: 3.666A pdb=" N GLN R 365 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL R 398 " --> pdb=" O LEU R 450 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU R 450 " --> pdb=" O VAL R 398 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY R 400 " --> pdb=" O ILE R 448 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE R 448 " --> pdb=" O GLY R 400 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU R 402 " --> pdb=" O ASN R 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 371 through 374 removed outlier: 3.782A pdb=" N GLY R 517 " --> pdb=" O THR R 524 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN R 526 " --> pdb=" O VAL R 515 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL R 515 " --> pdb=" O GLN R 526 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 436 through 438 removed outlier: 4.520A pdb=" N SER R 532 " --> pdb=" O TRP R 498 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA R 538 " --> pdb=" O GLU R 492 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU R 492 " --> pdb=" O ALA R 538 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 749 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: 1.22 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1088 1.33 - 1.46: 869 1.46 - 1.58: 2301 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 4296 Sorted by residual: bond pdb=" C ALA R 412 " pdb=" N ASN R 413 " ideal model delta sigma weight residual 1.332 1.576 -0.244 1.40e-02 5.10e+03 3.03e+02 bond pdb=" C LYS R 519 " pdb=" N ASN R 520 " ideal model delta sigma weight residual 1.333 1.444 -0.111 1.39e-02 5.18e+03 6.42e+01 bond pdb=" C GLN R 405 " pdb=" N ASN R 406 " ideal model delta sigma weight residual 1.330 1.269 0.061 1.52e-02 4.33e+03 1.60e+01 bond pdb=" C ASN R 406 " pdb=" N MET R 407 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.33e-02 5.65e+03 4.74e+00 bond pdb=" C ASN R 520 " pdb=" N GLY R 521 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.32e-02 5.74e+03 4.17e+00 ... (remaining 4291 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.58: 113 106.58 - 113.46: 2394 113.46 - 120.34: 1558 120.34 - 127.22: 1716 127.22 - 134.09: 56 Bond angle restraints: 5837 Sorted by residual: angle pdb=" CA GLN R 405 " pdb=" C GLN R 405 " pdb=" N ASN R 406 " ideal model delta sigma weight residual 118.21 126.57 -8.36 1.36e+00 5.41e-01 3.78e+01 angle pdb=" O GLN R 405 " pdb=" C GLN R 405 " pdb=" N ASN R 406 " ideal model delta sigma weight residual 122.46 114.48 7.98 1.37e+00 5.33e-01 3.40e+01 angle pdb=" C GLY R 647 " pdb=" N GLN R 648 " pdb=" CA GLN R 648 " ideal model delta sigma weight residual 121.54 129.73 -8.19 1.91e+00 2.74e-01 1.84e+01 angle pdb=" CA LEU R 549 " pdb=" CB LEU R 549 " pdb=" CG LEU R 549 " ideal model delta sigma weight residual 116.30 125.69 -9.39 3.50e+00 8.16e-02 7.20e+00 angle pdb=" CA MET R 537 " pdb=" CB MET R 537 " pdb=" CG MET R 537 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.13e+00 ... (remaining 5832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 2306 14.04 - 28.08: 193 28.08 - 42.11: 61 42.11 - 56.15: 14 56.15 - 70.18: 6 Dihedral angle restraints: 2580 sinusoidal: 1048 harmonic: 1532 Sorted by residual: dihedral pdb=" CA ASP R 761 " pdb=" C ASP R 761 " pdb=" N ASP R 762 " pdb=" CA ASP R 762 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA MET R 537 " pdb=" C MET R 537 " pdb=" N ALA R 538 " pdb=" CA ALA R 538 " ideal model delta harmonic sigma weight residual 180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB CYS R 612 " pdb=" SG CYS R 612 " pdb=" SG CYS R 684 " pdb=" CB CYS R 684 " ideal model delta sinusoidal sigma weight residual -86.00 -116.85 30.85 1 1.00e+01 1.00e-02 1.36e+01 ... (remaining 2577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 684 0.302 - 0.603: 0 0.603 - 0.905: 0 0.905 - 1.206: 1 1.206 - 1.508: 1 Chirality restraints: 686 Sorted by residual: chirality pdb=" C1 NAG R 902 " pdb=" ND2 ASN R 406 " pdb=" C2 NAG R 902 " pdb=" O5 NAG R 902 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.68e+01 chirality pdb=" C1 NAG R 903 " pdb=" ND2 ASN R 520 " pdb=" C2 NAG R 903 " pdb=" O5 NAG R 903 " both_signs ideal model delta sigma weight residual False -2.40 -1.35 -1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA MET R 537 " pdb=" N MET R 537 " pdb=" C MET R 537 " pdb=" CB MET R 537 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 683 not shown) Planarity restraints: 727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 413 " -0.128 2.00e-02 2.50e+03 1.43e-01 2.55e+02 pdb=" CG ASN R 413 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN R 413 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN R 413 " 0.228 2.00e-02 2.50e+03 pdb=" C1 NAG R 901 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 348 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C GLY R 348 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY R 348 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO R 349 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 319 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO R 320 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 320 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 320 " -0.039 5.00e-02 4.00e+02 ... (remaining 724 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 106 2.71 - 3.26: 4103 3.26 - 3.80: 6903 3.80 - 4.35: 8293 4.35 - 4.90: 14231 Nonbonded interactions: 33636 Sorted by model distance: nonbonded pdb=" O ARG R 643 " pdb=" NE2 GLN R 646 " model vdw 2.162 2.520 nonbonded pdb=" OG1 THR R 568 " pdb=" OH TYR R 797 " model vdw 2.181 2.440 nonbonded pdb=" O SER R 356 " pdb=" NE2 GLN R 405 " model vdw 2.201 2.520 nonbonded pdb=" NH1 ARG R 490 " pdb=" O GLY R 605 " model vdw 2.203 2.520 nonbonded pdb=" OE1 GLU R 295 " pdb=" NE2 GLN R 299 " model vdw 2.215 2.520 ... (remaining 33631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.500 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 : 0.005 0.244 4296 Z= 0.341 Angle : 0.697 9.389 5837 Z= 0.369 Chirality : 0.083 1.508 686 Planarity : 0.006 0.071 724 Dihedral : 12.439 70.184 1583 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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 (0.36), residues: 529 helix: 2.40 (0.31), residues: 266 sheet: 0.66 (0.58), residues: 78 loop : -0.79 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 498 HIS 0.002 0.000 HIS R 585 PHE 0.015 0.001 PHE R 627 TYR 0.009 0.001 TYR R 769 ARG 0.014 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.7964 (mtm) cc_final: 0.7721 (mtm) REVERT: R 338 MET cc_start: 0.8201 (mtm) cc_final: 0.7958 (mtm) REVERT: R 491 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6241 (tm-30) REVERT: R 537 MET cc_start: 0.5740 (tpt) cc_final: 0.5456 (tpt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2552 time to fit residues: 24.5808 Evaluate side-chains 76 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS R 299 GLN ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4296 Z= 0.291 Angle : 0.655 12.007 5837 Z= 0.326 Chirality : 0.044 0.285 686 Planarity : 0.005 0.060 724 Dihedral : 4.996 36.150 632 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.10 % Allowed : 6.36 % Favored : 92.54 % 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: 1.56 (0.36), residues: 529 helix: 2.24 (0.31), residues: 266 sheet: 0.63 (0.60), residues: 79 loop : -0.59 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 498 HIS 0.003 0.001 HIS R 539 PHE 0.015 0.002 PHE R 627 TYR 0.011 0.002 TYR R 660 ARG 0.007 0.000 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8097 (mtm) cc_final: 0.7845 (mtm) REVERT: R 338 MET cc_start: 0.8220 (mtm) cc_final: 0.7942 (mtm) REVERT: R 491 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6627 (tm-30) REVERT: R 537 MET cc_start: 0.5985 (tpt) cc_final: 0.5601 (tpt) REVERT: R 540 TYR cc_start: 0.7270 (m-10) cc_final: 0.6998 (m-10) REVERT: R 576 GLN cc_start: 0.6909 (mm110) cc_final: 0.6653 (mm110) REVERT: R 693 LEU cc_start: 0.7961 (tp) cc_final: 0.7753 (tp) outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.3051 time to fit residues: 28.2000 Evaluate side-chains 79 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 371 ASN Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 32 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4296 Z= 0.211 Angle : 0.608 10.709 5837 Z= 0.302 Chirality : 0.040 0.204 686 Planarity : 0.005 0.056 724 Dihedral : 4.589 28.153 632 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.75 % Allowed : 6.58 % Favored : 91.67 % 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: 1.66 (0.37), residues: 529 helix: 2.34 (0.31), residues: 267 sheet: 0.38 (0.58), residues: 79 loop : -0.42 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 498 HIS 0.003 0.000 HIS R 539 PHE 0.014 0.001 PHE R 627 TYR 0.006 0.001 TYR R 621 ARG 0.009 0.000 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8072 (mtm) cc_final: 0.7853 (mtm) REVERT: R 338 MET cc_start: 0.8228 (mtm) cc_final: 0.7929 (mtm) REVERT: R 423 GLN cc_start: 0.8619 (mt0) cc_final: 0.8346 (mt0) REVERT: R 491 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6574 (tm-30) REVERT: R 519 LYS cc_start: 0.8434 (tppt) cc_final: 0.8130 (tptp) REVERT: R 540 TYR cc_start: 0.7215 (m-10) cc_final: 0.6933 (m-10) REVERT: R 576 GLN cc_start: 0.6900 (mm110) cc_final: 0.6615 (mm110) REVERT: R 630 MET cc_start: 0.6566 (tpt) cc_final: 0.6326 (tpt) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 0.3165 time to fit residues: 30.2987 Evaluate side-chains 86 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 371 ASN Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 440 ARG Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 13 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 778 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4296 Z= 0.192 Angle : 0.591 10.576 5837 Z= 0.294 Chirality : 0.040 0.183 686 Planarity : 0.005 0.055 724 Dihedral : 4.350 23.048 632 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.32 % Allowed : 7.89 % Favored : 90.79 % 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: 1.76 (0.37), residues: 529 helix: 2.41 (0.31), residues: 268 sheet: 0.44 (0.60), residues: 79 loop : -0.37 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.012 0.001 PHE R 627 TYR 0.006 0.001 TYR R 683 ARG 0.009 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8043 (mtm) cc_final: 0.7827 (mtm) REVERT: R 338 MET cc_start: 0.8225 (mtm) cc_final: 0.7917 (mtm) REVERT: R 407 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6588 (mmp) REVERT: R 486 MET cc_start: 0.8919 (tmm) cc_final: 0.8259 (tmm) REVERT: R 540 TYR cc_start: 0.7226 (m-10) cc_final: 0.6918 (m-10) REVERT: R 576 GLN cc_start: 0.6883 (mm110) cc_final: 0.6587 (mm110) REVERT: R 792 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8220 (mtpp) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.2935 time to fit residues: 27.6378 Evaluate side-chains 77 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4296 Z= 0.253 Angle : 0.641 11.153 5837 Z= 0.317 Chirality : 0.041 0.177 686 Planarity : 0.005 0.054 724 Dihedral : 4.421 25.403 632 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.32 % Allowed : 8.33 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.37), residues: 529 helix: 2.24 (0.31), residues: 268 sheet: 0.23 (0.59), residues: 80 loop : -0.49 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 498 HIS 0.004 0.001 HIS R 539 PHE 0.012 0.001 PHE R 627 TYR 0.009 0.001 TYR R 683 ARG 0.007 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8101 (mtm) cc_final: 0.7877 (mtm) REVERT: R 338 MET cc_start: 0.8247 (mtm) cc_final: 0.7920 (mtm) REVERT: R 407 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6571 (mmp) REVERT: R 519 LYS cc_start: 0.8582 (tppt) cc_final: 0.8194 (tptp) REVERT: R 576 GLN cc_start: 0.6909 (mm110) cc_final: 0.6610 (mm110) REVERT: R 630 MET cc_start: 0.6703 (tpt) cc_final: 0.6490 (tpt) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.2813 time to fit residues: 26.0508 Evaluate side-chains 82 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 371 ASN Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4296 Z= 0.317 Angle : 0.656 10.866 5837 Z= 0.329 Chirality : 0.041 0.151 686 Planarity : 0.005 0.054 724 Dihedral : 4.483 22.803 632 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.32 % Allowed : 8.55 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.36), residues: 529 helix: 2.02 (0.31), residues: 268 sheet: 0.43 (0.60), residues: 74 loop : -0.63 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 498 HIS 0.004 0.001 HIS R 539 PHE 0.012 0.002 PHE R 781 TYR 0.009 0.001 TYR R 660 ARG 0.008 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 277 ARG cc_start: 0.7765 (mmm160) cc_final: 0.7557 (mmm160) REVERT: R 309 MET cc_start: 0.8168 (mtm) cc_final: 0.7934 (mtm) REVERT: R 338 MET cc_start: 0.8279 (mtm) cc_final: 0.7936 (mtm) REVERT: R 407 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6535 (mmp) REVERT: R 576 GLN cc_start: 0.6852 (mm110) cc_final: 0.6545 (mm110) REVERT: R 630 MET cc_start: 0.6663 (tpt) cc_final: 0.6261 (tpt) REVERT: R 745 GLN cc_start: 0.7457 (tt0) cc_final: 0.7162 (tt0) REVERT: R 792 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8361 (mtpp) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.2764 time to fit residues: 24.9499 Evaluate side-chains 80 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 371 ASN Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4296 Z= 0.273 Angle : 0.652 11.254 5837 Z= 0.328 Chirality : 0.041 0.164 686 Planarity : 0.005 0.055 724 Dihedral : 4.455 23.612 632 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.10 % Allowed : 9.87 % Favored : 89.04 % 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: 1.35 (0.37), residues: 529 helix: 2.06 (0.31), residues: 268 sheet: 0.20 (0.57), residues: 83 loop : -0.54 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.012 0.002 PHE R 781 TYR 0.007 0.001 TYR R 683 ARG 0.006 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8154 (mtm) cc_final: 0.7915 (mtm) REVERT: R 338 MET cc_start: 0.8273 (mtm) cc_final: 0.7922 (mtm) REVERT: R 407 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6499 (mmp) REVERT: R 576 GLN cc_start: 0.6837 (mm110) cc_final: 0.6541 (mm110) REVERT: R 745 GLN cc_start: 0.7449 (tt0) cc_final: 0.7181 (tt0) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.2949 time to fit residues: 26.4381 Evaluate side-chains 81 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 371 ASN Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.0060 chunk 25 optimal weight: 0.0270 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4296 Z= 0.192 Angle : 0.653 11.396 5837 Z= 0.320 Chirality : 0.040 0.159 686 Planarity : 0.005 0.056 724 Dihedral : 4.285 23.885 632 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.54 % Allowed : 9.43 % Favored : 89.04 % 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: 1.64 (0.37), residues: 529 helix: 2.32 (0.31), residues: 268 sheet: 0.26 (0.58), residues: 84 loop : -0.39 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 629 HIS 0.002 0.000 HIS R 539 PHE 0.009 0.001 PHE R 623 TYR 0.007 0.001 TYR R 683 ARG 0.009 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8101 (mtm) cc_final: 0.7895 (mtm) REVERT: R 338 MET cc_start: 0.8236 (mtm) cc_final: 0.7886 (mtm) REVERT: R 576 GLN cc_start: 0.6898 (mm110) cc_final: 0.6584 (mm110) REVERT: R 630 MET cc_start: 0.6716 (tpt) cc_final: 0.6514 (tpt) REVERT: R 792 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8372 (mttt) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.2911 time to fit residues: 25.4085 Evaluate side-chains 77 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 371 ASN Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 646 GLN Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4296 Z= 0.251 Angle : 0.658 11.382 5837 Z= 0.330 Chirality : 0.040 0.169 686 Planarity : 0.005 0.055 724 Dihedral : 4.241 23.636 632 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.54 % Allowed : 9.21 % Favored : 89.25 % 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: 1.61 (0.37), residues: 529 helix: 2.26 (0.31), residues: 268 sheet: 0.26 (0.58), residues: 83 loop : -0.36 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 498 HIS 0.002 0.000 HIS R 585 PHE 0.011 0.001 PHE R 645 TYR 0.006 0.001 TYR R 769 ARG 0.009 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8138 (mtm) cc_final: 0.7937 (mtm) REVERT: R 338 MET cc_start: 0.8255 (mtm) cc_final: 0.7906 (mtm) REVERT: R 630 MET cc_start: 0.6729 (tpt) cc_final: 0.6432 (tpt) REVERT: R 792 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8356 (mtpp) REVERT: R 798 ARG cc_start: 0.6371 (ppt170) cc_final: 0.5952 (ppt170) outliers start: 7 outliers final: 7 residues processed: 74 average time/residue: 0.2360 time to fit residues: 20.6414 Evaluate side-chains 80 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 MET Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 646 GLN Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.0010 chunk 6 optimal weight: 3.9990 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4296 Z= 0.199 Angle : 0.651 11.794 5837 Z= 0.321 Chirality : 0.040 0.182 686 Planarity : 0.005 0.056 724 Dihedral : 4.156 23.782 632 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.54 % Allowed : 9.21 % Favored : 89.25 % 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: 1.71 (0.37), residues: 529 helix: 2.37 (0.31), residues: 268 sheet: 0.30 (0.59), residues: 83 loop : -0.34 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 629 HIS 0.001 0.000 HIS R 539 PHE 0.010 0.001 PHE R 627 TYR 0.007 0.001 TYR R 683 ARG 0.009 0.001 ARG R 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8099 (mtm) cc_final: 0.7895 (mtm) REVERT: R 338 MET cc_start: 0.8259 (mtm) cc_final: 0.7908 (mtm) REVERT: R 630 MET cc_start: 0.6645 (tpt) cc_final: 0.6085 (mmm) REVERT: R 792 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8331 (mtpp) outliers start: 7 outliers final: 7 residues processed: 76 average time/residue: 0.3000 time to fit residues: 26.4531 Evaluate side-chains 78 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 371 ASN Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 646 GLN Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 0.0670 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.177298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124752 restraints weight = 16952.251| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.83 r_work: 0.3322 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4296 Z= 0.293 Angle : 0.718 16.839 5837 Z= 0.348 Chirality : 0.041 0.155 686 Planarity : 0.005 0.054 724 Dihedral : 4.229 23.328 632 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 9.87 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.37), residues: 529 helix: 2.13 (0.31), residues: 268 sheet: 0.21 (0.58), residues: 83 loop : -0.36 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 498 HIS 0.002 0.001 HIS R 585 PHE 0.012 0.002 PHE R 645 TYR 0.007 0.001 TYR R 769 ARG 0.009 0.001 ARG R 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.44 seconds wall clock time: 29 minutes 13.31 seconds (1753.31 seconds total)