Starting phenix.real_space_refine on Mon Sep 23 17:41:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/09_2024/8ikj_35514.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/09_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_35514/09_2024/8ikj_35514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/09_2024/8ikj_35514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/09_2024/8ikj_35514.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikj_35514/09_2024/8ikj_35514.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.55, per 1000 atoms: 1.08 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 - 3.00 Amino acid : True - 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: 0.88 Conformation dependent library (CDL) restraints added in 845.1 milliseconds 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: 0.40 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: 1.16 Time building geometry restraints manager: 1.07 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: 0.00 - 1.88: 5680 1.88 - 3.76: 126 3.76 - 5.63: 25 5.63 - 7.51: 2 7.51 - 9.39: 4 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 3.120 nonbonded pdb=" OG1 THR R 568 " pdb=" OH TYR R 797 " model vdw 2.181 3.040 nonbonded pdb=" O SER R 356 " pdb=" NE2 GLN R 405 " model vdw 2.201 3.120 nonbonded pdb=" NH1 ARG R 490 " pdb=" O GLY R 605 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLU R 295 " pdb=" NE2 GLN R 299 " model vdw 2.215 3.120 ... (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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- 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 : 0.453 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: 0.2998 time to fit residues: 28.7788 Evaluate side-chains 76 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 1.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4296 Z= 0.373 Angle : 0.706 12.433 5837 Z= 0.352 Chirality : 0.046 0.303 686 Planarity : 0.005 0.060 724 Dihedral : 5.112 37.506 632 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.32 % Allowed : 5.92 % Favored : 92.76 % 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: 1.32 (0.36), residues: 529 helix: 1.88 (0.30), residues: 269 sheet: 0.35 (0.59), residues: 84 loop : -0.37 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 498 HIS 0.003 0.001 HIS R 539 PHE 0.017 0.002 PHE R 627 TYR 0.014 0.002 TYR R 660 ARG 0.007 0.001 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 85 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8146 (mtm) cc_final: 0.7881 (mtm) REVERT: R 338 MET cc_start: 0.8278 (mtm) cc_final: 0.7991 (mtm) REVERT: R 407 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6503 (mmp) REVERT: R 491 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6711 (tm-30) REVERT: R 537 MET cc_start: 0.5917 (tpt) cc_final: 0.5516 (tpt) REVERT: R 540 TYR cc_start: 0.7279 (m-10) cc_final: 0.6993 (m-10) REVERT: R 544 ASP cc_start: 0.6393 (p0) cc_final: 0.6174 (p0) REVERT: R 576 GLN cc_start: 0.6853 (mm110) cc_final: 0.6601 (mm110) REVERT: R 693 LEU cc_start: 0.7917 (tp) cc_final: 0.7711 (tp) REVERT: R 792 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8272 (mtpp) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 0.2211 time to fit residues: 21.4291 Evaluate side-chains 81 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 791 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 40 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4296 Z= 0.238 Angle : 0.633 10.885 5837 Z= 0.318 Chirality : 0.042 0.224 686 Planarity : 0.005 0.055 724 Dihedral : 5.040 44.684 632 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.10 % Allowed : 6.58 % Favored : 92.32 % 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: 1.57 (0.37), residues: 529 helix: 2.22 (0.31), residues: 262 sheet: 0.44 (0.60), residues: 79 loop : -0.36 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 498 HIS 0.003 0.000 HIS R 539 PHE 0.013 0.001 PHE R 627 TYR 0.007 0.001 TYR R 769 ARG 0.002 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: 5 poor density : 84 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8086 (mtm) cc_final: 0.7819 (mtm) REVERT: R 338 MET cc_start: 0.8263 (mtm) cc_final: 0.7959 (mtm) REVERT: R 407 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6509 (mmp) REVERT: R 423 GLN cc_start: 0.8623 (mt0) cc_final: 0.8358 (mt0) REVERT: R 491 GLN cc_start: 0.7135 (tm-30) cc_final: 0.6756 (tm-30) REVERT: R 540 TYR cc_start: 0.7270 (m-10) cc_final: 0.7011 (m-10) REVERT: R 576 GLN cc_start: 0.6851 (mm110) cc_final: 0.6559 (mm110) REVERT: R 630 MET cc_start: 0.6763 (tpt) cc_final: 0.6553 (tpt) REVERT: R 792 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8327 (mtpp) outliers start: 5 outliers final: 3 residues processed: 86 average time/residue: 0.2731 time to fit residues: 27.1385 Evaluate side-chains 83 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 778 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4296 Z= 0.258 Angle : 0.648 10.412 5837 Z= 0.326 Chirality : 0.042 0.187 686 Planarity : 0.005 0.054 724 Dihedral : 4.858 40.004 632 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 1.50 (0.37), residues: 529 helix: 2.15 (0.31), residues: 262 sheet: 0.41 (0.61), residues: 79 loop : -0.37 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.024 0.002 PHE R 623 TYR 0.008 0.001 TYR R 769 ARG 0.010 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 88 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8109 (mtm) cc_final: 0.7844 (mtm) REVERT: R 338 MET cc_start: 0.8280 (mtm) cc_final: 0.7968 (mtm) REVERT: R 407 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6703 (mmp) REVERT: R 430 TYR cc_start: 0.7528 (m-10) cc_final: 0.7273 (m-10) REVERT: R 540 TYR cc_start: 0.7323 (m-10) cc_final: 0.6932 (m-10) REVERT: R 544 ASP cc_start: 0.6403 (p0) cc_final: 0.6099 (p0) REVERT: R 576 GLN cc_start: 0.6841 (mm110) cc_final: 0.6535 (mm110) REVERT: R 745 GLN cc_start: 0.7451 (tt0) cc_final: 0.7195 (tt0) REVERT: R 792 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8313 (mtpp) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.2747 time to fit residues: 26.8338 Evaluate side-chains 80 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 0.8980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4296 Z= 0.284 Angle : 0.678 11.084 5837 Z= 0.337 Chirality : 0.041 0.191 686 Planarity : 0.005 0.054 724 Dihedral : 4.749 36.638 632 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.10 % Allowed : 8.99 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.37), residues: 529 helix: 2.10 (0.30), residues: 262 sheet: 0.23 (0.59), residues: 80 loop : -0.47 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 498 HIS 0.003 0.001 HIS R 539 PHE 0.024 0.002 PHE R 623 TYR 0.008 0.001 TYR R 769 ARG 0.011 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 81 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8115 (mtm) cc_final: 0.7882 (mtm) REVERT: R 338 MET cc_start: 0.8279 (mtm) cc_final: 0.7969 (mtm) REVERT: R 407 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6296 (mmp) REVERT: R 540 TYR cc_start: 0.7318 (m-10) cc_final: 0.7073 (m-10) REVERT: R 544 ASP cc_start: 0.6293 (p0) cc_final: 0.5987 (p0) REVERT: R 576 GLN cc_start: 0.6890 (mm110) cc_final: 0.6589 (mm110) REVERT: R 630 MET cc_start: 0.6792 (tpt) cc_final: 0.6302 (tpt) REVERT: R 792 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8364 (mtpp) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.2635 time to fit residues: 24.2888 Evaluate side-chains 82 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 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 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4296 Z= 0.248 Angle : 0.680 11.114 5837 Z= 0.337 Chirality : 0.041 0.179 686 Planarity : 0.004 0.053 724 Dihedral : 4.503 26.952 632 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.32 % Allowed : 10.31 % Favored : 88.38 % 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: 1.43 (0.36), residues: 529 helix: 2.18 (0.31), residues: 262 sheet: 0.48 (0.61), residues: 74 loop : -0.58 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 498 HIS 0.003 0.000 HIS R 539 PHE 0.023 0.002 PHE R 623 TYR 0.008 0.001 TYR R 769 ARG 0.003 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 : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8100 (mtm) cc_final: 0.7857 (mtm) REVERT: R 338 MET cc_start: 0.8267 (mtm) cc_final: 0.7953 (mtm) REVERT: R 407 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6250 (mmp) REVERT: R 540 TYR cc_start: 0.7377 (m-10) cc_final: 0.7021 (m-10) REVERT: R 544 ASP cc_start: 0.6288 (p0) cc_final: 0.5995 (p0) REVERT: R 576 GLN cc_start: 0.6896 (mm110) cc_final: 0.6596 (mm110) REVERT: R 630 MET cc_start: 0.6853 (tpt) cc_final: 0.6572 (mmm) REVERT: R 792 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8359 (mtpp) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.2701 time to fit residues: 24.7863 Evaluate side-chains 79 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4296 Z= 0.287 Angle : 0.695 10.999 5837 Z= 0.347 Chirality : 0.041 0.163 686 Planarity : 0.004 0.053 724 Dihedral : 4.455 23.265 632 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.10 % Allowed : 10.53 % Favored : 88.38 % 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: 1.36 (0.36), residues: 529 helix: 2.07 (0.31), residues: 262 sheet: 0.56 (0.61), residues: 74 loop : -0.59 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.024 0.002 PHE R 623 TYR 0.009 0.001 TYR R 769 ARG 0.009 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 82 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8123 (mtm) cc_final: 0.7876 (mtm) REVERT: R 338 MET cc_start: 0.8275 (mtm) cc_final: 0.7955 (mtm) REVERT: R 407 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6224 (mmp) REVERT: R 540 TYR cc_start: 0.7420 (m-10) cc_final: 0.7122 (m-10) REVERT: R 544 ASP cc_start: 0.6276 (p0) cc_final: 0.6006 (p0) REVERT: R 576 GLN cc_start: 0.6903 (mm110) cc_final: 0.6601 (mm110) REVERT: R 630 MET cc_start: 0.7029 (tpt) cc_final: 0.6799 (mmm) REVERT: R 792 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8385 (mtpp) outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.2766 time to fit residues: 25.6834 Evaluate side-chains 81 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 791 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4296 Z= 0.239 Angle : 0.684 11.436 5837 Z= 0.341 Chirality : 0.041 0.170 686 Planarity : 0.004 0.052 724 Dihedral : 4.368 23.215 632 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.88 % Allowed : 11.18 % Favored : 87.94 % 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 (0.37), residues: 529 helix: 2.26 (0.31), residues: 262 sheet: 0.34 (0.59), residues: 84 loop : -0.40 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 498 HIS 0.003 0.000 HIS R 539 PHE 0.025 0.001 PHE R 623 TYR 0.007 0.001 TYR R 769 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 78 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8087 (mtm) cc_final: 0.7830 (mtm) REVERT: R 338 MET cc_start: 0.8246 (mtm) cc_final: 0.7927 (mtm) REVERT: R 407 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6133 (mmp) REVERT: R 544 ASP cc_start: 0.6393 (p0) cc_final: 0.6048 (p0) REVERT: R 576 GLN cc_start: 0.6860 (mm110) cc_final: 0.6541 (mm110) REVERT: R 613 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7508 (mtp85) REVERT: R 792 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8362 (mtpp) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.2793 time to fit residues: 24.5400 Evaluate side-chains 78 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 791 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.0470 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4296 Z= 0.235 Angle : 0.736 17.833 5837 Z= 0.357 Chirality : 0.042 0.188 686 Planarity : 0.004 0.052 724 Dihedral : 4.363 23.416 632 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.88 % Allowed : 11.62 % Favored : 87.50 % 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 (0.37), residues: 529 helix: 2.29 (0.31), residues: 262 sheet: 0.17 (0.58), residues: 84 loop : -0.37 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.025 0.001 PHE R 623 TYR 0.013 0.001 TYR R 683 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 73 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: R 309 MET cc_start: 0.8112 (mtm) cc_final: 0.7842 (mtm) REVERT: R 338 MET cc_start: 0.8273 (mtm) cc_final: 0.7966 (mtm) REVERT: R 407 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6134 (mmp) REVERT: R 576 GLN cc_start: 0.6861 (mm110) cc_final: 0.6532 (mm110) REVERT: R 613 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7503 (mtp85) REVERT: R 680 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7859 (mtp85) REVERT: R 792 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8301 (mtpp) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.2843 time to fit residues: 23.3160 Evaluate side-chains 72 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 33 optimal weight: 0.0980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.0010 chunk 6 optimal weight: 4.9990 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 745 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4296 Z= 0.209 Angle : 0.726 16.778 5837 Z= 0.352 Chirality : 0.041 0.182 686 Planarity : 0.004 0.052 724 Dihedral : 4.226 23.180 632 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.66 % Allowed : 12.06 % Favored : 87.28 % 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 (0.37), residues: 529 helix: 2.35 (0.31), residues: 262 sheet: 0.13 (0.58), residues: 84 loop : -0.38 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.026 0.001 PHE R 623 TYR 0.011 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 71 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 338 MET cc_start: 0.8246 (mtm) cc_final: 0.7948 (mtm) REVERT: R 407 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6005 (mmp) REVERT: R 576 GLN cc_start: 0.6851 (mm110) cc_final: 0.6519 (mm110) REVERT: R 680 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7797 (mtp85) REVERT: R 792 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8166 (mtpp) outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 0.2890 time to fit residues: 23.3756 Evaluate side-chains 72 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.0270 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 28 optimal weight: 0.4980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.178840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126929 restraints weight = 17024.507| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 4.89 r_work: 0.3335 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4296 Z= 0.237 Angle : 0.741 16.655 5837 Z= 0.364 Chirality : 0.042 0.163 686 Planarity : 0.004 0.051 724 Dihedral : 4.326 23.326 632 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.66 % Allowed : 12.72 % Favored : 86.62 % 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: 1.54 (0.37), residues: 529 helix: 2.34 (0.31), residues: 262 sheet: 0.04 (0.58), residues: 84 loop : -0.42 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 685 HIS 0.002 0.000 HIS R 585 PHE 0.027 0.001 PHE R 623 TYR 0.010 0.001 TYR R 683 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: 1462.06 seconds wall clock time: 29 minutes 37.10 seconds (1777.10 seconds total)