Starting phenix.real_space_refine on Fri Aug 2 20:11:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5a_44205/08_2024/9b5a_44205.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5a_44205/08_2024/9b5a_44205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5a_44205/08_2024/9b5a_44205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5a_44205/08_2024/9b5a_44205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5a_44205/08_2024/9b5a_44205.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5a_44205/08_2024/9b5a_44205.cif" } resolution = 3.65 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= 0.038 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 14 5.16 5 C 3110 2.51 5 N 824 2.21 5 O 923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 3107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} Conformer: "B" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} bond proxies already assigned to first conformer: 3161 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.99 Number of scatterers: 4871 At special positions: 0 Unit cell: (74.48, 82.992, 97.888, 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 14 16.00 O 923 8.00 N 824 7.00 C 3110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 49.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.834A pdb=" N ASP A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 112 removed outlier: 3.786A pdb=" N VAL A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 308 through 311 removed outlier: 3.835A pdb=" N ALA C 311 " --> pdb=" O PRO C 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 311' Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.577A pdb=" N SER C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.520A pdb=" N LYS C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 374 Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.951A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 400 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.070A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.539A pdb=" N TYR C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.007A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.784A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE C 495 " --> pdb=" O GLY C 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 491 through 495' Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 558 through 564 Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.592A pdb=" N ILE C 578 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 601 Processing helix chain 'C' and resid 608 through 613 removed outlier: 3.917A pdb=" N LYS C 611 " --> pdb=" O SER C 608 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP C 612 " --> pdb=" O GLY C 609 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET C 613 " --> pdb=" O PHE C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 613' Processing helix chain 'C' and resid 638 through 640 No H-bonds generated for 'chain 'C' and resid 638 through 640' Processing helix chain 'C' and resid 650 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321 removed outlier: 3.533A pdb=" N VAL C 321 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AA5, first strand: chain 'C' and resid 475 through 479 removed outlier: 3.773A pdb=" N GLU C 482 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568 removed outlier: 6.536A pdb=" N ASP C 566 " --> pdb=" O ILE C 624 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 608 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: 1.25 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 820 1.27 - 1.41: 1239 1.41 - 1.54: 2895 1.54 - 1.68: 5 1.68 - 1.82: 24 Bond restraints: 4983 Sorted by residual: bond pdb=" C04 A1AIV B 101 " pdb=" C05 A1AIV B 101 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.10e-01 bond pdb=" CG LEU C 595 " pdb=" CD2 LEU C 595 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.69e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 100.21 - 116.11: 3268 116.11 - 132.00: 3470 132.00 - 147.89: 8 147.89 - 163.78: 0 163.78 - 179.67: 1 Bond angle restraints: 6747 Sorted by residual: angle pdb=" N LEU C 424 " pdb=" CA LEU C 424 " pdb=" C LEU C 424 " ideal model delta sigma weight residual 110.41 108.27 2.14 1.23e+00 6.61e-01 3.03e+00 angle pdb=" C LEU C 424 " pdb=" N ASP C 425 " pdb=" CA ASP C 425 " ideal model delta sigma weight residual 122.62 120.33 2.29 1.63e+00 3.76e-01 1.97e+00 angle pdb=" CA TRP C 581 " pdb=" CB TRP C 581 " pdb=" CG TRP C 581 " ideal model delta sigma weight residual 113.60 110.94 2.66 1.90e+00 2.77e-01 1.96e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 111.85 -2.51 2.08e+00 2.31e-01 1.45e+00 angle pdb=" N TYR C 423 " pdb=" CA TYR C 423 " pdb=" C TYR C 423 " ideal model delta sigma weight residual 108.52 110.46 -1.94 1.63e+00 3.76e-01 1.42e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.48: 2647 11.48 - 22.97: 278 22.97 - 34.45: 73 34.45 - 45.94: 17 45.94 - 57.42: 3 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA TYR C 423 " pdb=" C TYR C 423 " pdb=" N LEU C 424 " pdb=" CA LEU C 424 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA VAL C 515 " pdb=" C VAL C 515 " pdb=" N THR C 516 " pdb=" CA THR C 516 " ideal model delta harmonic sigma weight residual -180.00 -164.52 -15.48 0 5.00e+00 4.00e-02 9.58e+00 dihedral pdb=" N LEU C 509 " pdb=" CA LEU C 509 " pdb=" CB LEU C 509 " pdb=" CG LEU C 509 " ideal model delta sinusoidal sigma weight residual -60.00 -110.67 50.67 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 443 0.027 - 0.054: 197 0.054 - 0.081: 49 0.081 - 0.107: 31 0.107 - 0.134: 17 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE C 533 " pdb=" N ILE C 533 " pdb=" C ILE C 533 " pdb=" CB ILE C 533 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE B 44 " pdb=" N ILE B 44 " pdb=" C ILE B 44 " pdb=" CB ILE B 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 76 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 94 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 95 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO C 431 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 431 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 431 " 0.016 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 12 2.40 - 3.03: 2981 3.03 - 3.65: 6872 3.65 - 4.28: 10171 4.28 - 4.90: 17504 Nonbonded interactions: 37540 Sorted by model distance: nonbonded pdb=" SG CYS A 85 " pdb=" C03 A1AIV B 101 " model vdw 1.776 3.800 nonbonded pdb=" OG SER C 397 " pdb=" OE1 GLN C 521 " model vdw 2.209 3.040 nonbonded pdb=" N ASP C 387 " pdb=" OD1 ASP C 387 " model vdw 2.263 3.120 nonbonded pdb=" O VAL C 426 " pdb=" ND2 ASN C 551 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASP C 487 " pdb=" NH2 ARG C 493 " model vdw 2.344 3.120 ... (remaining 37535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.010 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.910 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4983 Z= 0.225 Angle : 0.471 4.126 6747 Z= 0.242 Chirality : 0.039 0.134 737 Planarity : 0.003 0.038 873 Dihedral : 10.281 57.421 1878 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.66 % Allowed : 5.34 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.36), residues: 594 helix: 1.98 (0.34), residues: 254 sheet: 0.84 (0.60), residues: 84 loop : -0.40 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 581 HIS 0.005 0.001 HIS C 512 PHE 0.010 0.001 PHE C 407 TYR 0.011 0.001 TYR A 60 ARG 0.003 0.000 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8913 (tpp80) cc_final: 0.8711 (mmm-85) REVERT: A 135 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8075 (mt-10) REVERT: C 386 ASP cc_start: 0.8388 (m-30) cc_final: 0.8134 (m-30) REVERT: C 451 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7630 (mp0) REVERT: C 570 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.5058 (m-80) outliers start: 9 outliers final: 3 residues processed: 96 average time/residue: 0.2689 time to fit residues: 30.6708 Evaluate side-chains 55 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.0470 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.7246 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4983 Z= 0.231 Angle : 0.544 6.047 6747 Z= 0.283 Chirality : 0.040 0.134 737 Planarity : 0.004 0.039 873 Dihedral : 5.689 72.724 667 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.92 % Allowed : 11.42 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.19 (0.36), residues: 594 helix: 1.94 (0.34), residues: 262 sheet: 0.83 (0.58), residues: 89 loop : -0.48 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 581 HIS 0.003 0.001 HIS A 75 PHE 0.010 0.001 PHE C 622 TYR 0.017 0.001 TYR C 454 ARG 0.006 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8530 (mmm-85) REVERT: B 1 MET cc_start: 0.0620 (ptt) cc_final: 0.0042 (ppp) REVERT: B 61 ILE cc_start: -0.0593 (mt) cc_final: -0.0983 (mt) REVERT: B 74 ARG cc_start: 0.7083 (tpp80) cc_final: 0.6684 (mpt180) REVERT: C 343 LYS cc_start: 0.8916 (mttt) cc_final: 0.8208 (mtpp) REVERT: C 570 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.5069 (m-80) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.2247 time to fit residues: 15.8906 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7241 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4983 Z= 0.196 Angle : 0.503 6.405 6747 Z= 0.261 Chirality : 0.040 0.141 737 Planarity : 0.004 0.033 873 Dihedral : 5.784 77.738 664 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.66 % Allowed : 9.94 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.14 (0.36), residues: 594 helix: 1.85 (0.34), residues: 262 sheet: 0.91 (0.57), residues: 88 loop : -0.49 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 581 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE C 640 TYR 0.010 0.001 TYR A 60 ARG 0.004 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8163 (tmtt) REVERT: A 131 ARG cc_start: 0.8835 (tpp80) cc_final: 0.8534 (mmm-85) REVERT: B 61 ILE cc_start: -0.0504 (mt) cc_final: -0.0867 (mt) REVERT: B 74 ARG cc_start: 0.7077 (tpp80) cc_final: 0.6729 (mpt180) REVERT: C 343 LYS cc_start: 0.8898 (mttt) cc_final: 0.8306 (mtpp) REVERT: C 570 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.5170 (m-80) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.2138 time to fit residues: 15.0824 Evaluate side-chains 51 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7238 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4983 Z= 0.175 Angle : 0.487 5.888 6747 Z= 0.254 Chirality : 0.040 0.146 737 Planarity : 0.004 0.040 873 Dihedral : 5.789 79.630 664 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.10 % Allowed : 11.23 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.37), residues: 594 helix: 1.93 (0.34), residues: 262 sheet: 0.91 (0.58), residues: 89 loop : -0.46 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.003 0.000 HIS A 75 PHE 0.009 0.001 PHE C 640 TYR 0.017 0.001 TYR C 454 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7436 (tttt) REVERT: A 15 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8235 (tmtt) REVERT: A 131 ARG cc_start: 0.8826 (tpp80) cc_final: 0.8598 (mmm-85) REVERT: A 135 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7776 (tp30) REVERT: B 74 ARG cc_start: 0.7053 (tpp80) cc_final: 0.6760 (mpt180) REVERT: C 304 MET cc_start: 0.8927 (ttp) cc_final: 0.8502 (ttp) REVERT: C 343 LYS cc_start: 0.8894 (mttt) cc_final: 0.8189 (mtpp) REVERT: C 506 LEU cc_start: 0.7845 (mt) cc_final: 0.7533 (mp) REVERT: C 570 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.4843 (m-80) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.2414 time to fit residues: 15.6212 Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7260 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4983 Z= 0.222 Angle : 0.489 7.708 6747 Z= 0.255 Chirality : 0.040 0.138 737 Planarity : 0.004 0.048 873 Dihedral : 5.875 81.109 664 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.84 % Allowed : 11.79 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.36), residues: 594 helix: 1.70 (0.34), residues: 268 sheet: 0.77 (0.60), residues: 84 loop : -0.84 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.004 0.001 HIS A 125 PHE 0.010 0.001 PHE C 640 TYR 0.022 0.001 TYR C 454 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8260 (tmtt) REVERT: A 135 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7843 (tp30) REVERT: B 74 ARG cc_start: 0.7093 (tpp80) cc_final: 0.6808 (mpt180) REVERT: C 304 MET cc_start: 0.8945 (ttp) cc_final: 0.8512 (ttp) REVERT: C 343 LYS cc_start: 0.8909 (mttt) cc_final: 0.8210 (mtpp) REVERT: C 570 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.4942 (m-80) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.2209 time to fit residues: 14.5138 Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 0.0370 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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: 0.7230 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4983 Z= 0.140 Angle : 0.461 7.086 6747 Z= 0.239 Chirality : 0.039 0.146 737 Planarity : 0.004 0.044 873 Dihedral : 5.831 84.449 664 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.29 % Allowed : 11.97 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.16 (0.36), residues: 594 helix: 1.85 (0.34), residues: 262 sheet: 1.00 (0.58), residues: 89 loop : -0.51 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.004 0.001 HIS A 125 PHE 0.010 0.001 PHE C 640 TYR 0.024 0.001 TYR C 454 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8229 (mmmm) cc_final: 0.7569 (tttt) REVERT: A 15 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8247 (tmtt) REVERT: A 135 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7896 (tp30) REVERT: C 304 MET cc_start: 0.8903 (ttp) cc_final: 0.8506 (ttp) REVERT: C 343 LYS cc_start: 0.8898 (mttt) cc_final: 0.8184 (mtpp) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.2457 time to fit residues: 15.1645 Evaluate side-chains 43 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7258 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4983 Z= 0.213 Angle : 0.489 6.980 6747 Z= 0.254 Chirality : 0.041 0.146 737 Planarity : 0.004 0.042 873 Dihedral : 5.693 89.212 662 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.29 % Allowed : 12.15 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.36), residues: 594 helix: 1.69 (0.34), residues: 268 sheet: 0.86 (0.61), residues: 84 loop : -0.82 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 141 HIS 0.003 0.001 HIS A 75 PHE 0.008 0.001 PHE C 640 TYR 0.023 0.002 TYR C 454 ARG 0.004 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8274 (tmtt) REVERT: C 304 MET cc_start: 0.8938 (ttp) cc_final: 0.8512 (ttp) REVERT: C 343 LYS cc_start: 0.8915 (mttt) cc_final: 0.8278 (mtpp) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1890 time to fit residues: 11.9106 Evaluate side-chains 44 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7262 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4983 Z= 0.211 Angle : 0.494 7.118 6747 Z= 0.257 Chirality : 0.040 0.137 737 Planarity : 0.004 0.053 873 Dihedral : 5.722 86.786 662 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.29 % Allowed : 12.52 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.36), residues: 594 helix: 1.64 (0.34), residues: 268 sheet: 0.83 (0.61), residues: 84 loop : -0.87 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 141 HIS 0.003 0.001 HIS A 75 PHE 0.011 0.001 PHE C 640 TYR 0.024 0.001 TYR C 454 ARG 0.005 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8258 (tmtt) REVERT: C 343 LYS cc_start: 0.8910 (mttt) cc_final: 0.8265 (mtpp) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.2062 time to fit residues: 12.7940 Evaluate side-chains 45 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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: 0.7259 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4983 Z= 0.196 Angle : 0.493 7.310 6747 Z= 0.256 Chirality : 0.040 0.167 737 Planarity : 0.004 0.058 873 Dihedral : 5.637 85.001 662 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.10 % Allowed : 12.52 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.36), residues: 594 helix: 1.67 (0.34), residues: 268 sheet: 0.88 (0.61), residues: 84 loop : -0.86 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 141 HIS 0.002 0.001 HIS A 75 PHE 0.011 0.001 PHE C 640 TYR 0.024 0.001 TYR C 454 ARG 0.009 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8283 (mmmm) cc_final: 0.7570 (tttt) REVERT: A 15 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8279 (tmtt) REVERT: C 343 LYS cc_start: 0.8910 (mttt) cc_final: 0.8263 (mtpp) outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.1924 time to fit residues: 11.6211 Evaluate side-chains 44 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.0060 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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: 0.7248 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4983 Z= 0.165 Angle : 0.487 7.454 6747 Z= 0.255 Chirality : 0.040 0.160 737 Planarity : 0.004 0.059 873 Dihedral : 5.535 82.273 662 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.10 % Allowed : 12.34 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.36), residues: 594 helix: 1.72 (0.34), residues: 268 sheet: 0.99 (0.59), residues: 89 loop : -0.75 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 141 HIS 0.003 0.001 HIS A 75 PHE 0.014 0.001 PHE C 640 TYR 0.025 0.001 TYR C 454 ARG 0.007 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7574 (tttt) REVERT: A 15 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8277 (tmtt) REVERT: A 135 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8177 (tp30) REVERT: C 343 LYS cc_start: 0.8902 (mttt) cc_final: 0.8255 (mtpp) outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 0.2157 time to fit residues: 12.6968 Evaluate side-chains 44 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.116598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082762 restraints weight = 26270.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086356 restraints weight = 13915.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088968 restraints weight = 9158.355| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4983 Z= 0.185 Angle : 0.486 7.367 6747 Z= 0.253 Chirality : 0.040 0.157 737 Planarity : 0.004 0.060 873 Dihedral : 5.505 80.866 662 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.10 % Allowed : 12.34 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.36), residues: 594 helix: 1.74 (0.34), residues: 268 sheet: 0.96 (0.59), residues: 89 loop : -0.80 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 141 HIS 0.003 0.001 HIS A 75 PHE 0.022 0.001 PHE B 4 TYR 0.025 0.001 TYR C 454 ARG 0.010 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1405.30 seconds wall clock time: 25 minutes 32.75 seconds (1532.75 seconds total)