Starting phenix.real_space_refine on Fri Aug 2 20:05:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b57_44202/08_2024/9b57_44202.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b57_44202/08_2024/9b57_44202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b57_44202/08_2024/9b57_44202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b57_44202/08_2024/9b57_44202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b57_44202/08_2024/9b57_44202.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b57_44202/08_2024/9b57_44202.cif" } resolution = 3.37 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= 0.039 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 None Time to flip residues: 0.01s 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: 5.21, per 1000 atoms: 1.07 Number of scatterers: 4871 At special positions: 0 Unit cell: (63.84, 82.992, 103.208, 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: 1.87 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: 28 helices and 6 sheets defined 48.4% alpha, 11.9% 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 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.827A 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 37 through 41 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 338 through 343 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: 3.547A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.472A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.610A 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: 3.816A 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: 3.937A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 518 through 533 removed outlier: 4.315A pdb=" N LEU C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.585A pdb=" N LEU C 538 " --> pdb=" O PRO C 534 " (cutoff:3.500A) 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: 3.893A pdb=" N PHE C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 600 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 removed outlier: 3.569A pdb=" N ILE C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.963A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 321 removed outlier: 3.707A 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: 3.675A 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 568 223 hydrogen bonds defined for protein. 623 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: 1.23 Time building geometry restraints manager: 2.06 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: 1241 1.41 - 1.55: 2898 1.55 - 1.69: 0 1.69 - 1.83: 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 1.526 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 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=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.133 0.018 2.00e-02 2.50e+03 8.36e-01 bond pdb=" CG LEU C 595 " pdb=" CD2 LEU C 595 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.35e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 100.57 - 116.44: 3348 116.44 - 132.31: 3390 132.31 - 148.18: 8 148.18 - 164.04: 0 164.04 - 179.91: 1 Bond angle restraints: 6747 Sorted by residual: angle pdb=" C03 A1AIV B 101 " pdb=" C02 A1AIV B 101 " pdb=" N01 A1AIV B 101 " ideal model delta sigma weight residual 111.06 105.80 5.26 3.00e+00 1.11e-01 3.07e+00 angle pdb=" N LEU C 424 " pdb=" CA LEU C 424 " pdb=" C LEU C 424 " ideal model delta sigma weight residual 110.35 108.12 2.23 1.38e+00 5.25e-01 2.62e+00 angle pdb=" CA CYS C 639 " pdb=" CB CYS C 639 " pdb=" SG CYS C 639 " ideal model delta sigma weight residual 114.40 117.45 -3.05 2.30e+00 1.89e-01 1.76e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 112.04 -2.70 2.08e+00 2.31e-01 1.68e+00 angle pdb=" CA GLU C 586 " pdb=" CB GLU C 586 " pdb=" CG GLU C 586 " ideal model delta sigma weight residual 114.10 116.34 -2.24 2.00e+00 2.50e-01 1.25e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.29: 2740 13.29 - 26.59: 223 26.59 - 39.88: 44 39.88 - 53.17: 9 53.17 - 66.46: 2 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 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+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 -163.88 -16.12 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP C 357 " pdb=" CB ASP C 357 " pdb=" CG ASP C 357 " pdb=" OD1 ASP C 357 " ideal model delta sinusoidal sigma weight residual -30.00 -81.99 51.99 1 2.00e+01 2.50e-03 9.22e+00 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 443 0.027 - 0.054: 192 0.054 - 0.081: 59 0.081 - 0.109: 25 0.109 - 0.136: 18 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE C 645 " pdb=" N ILE C 645 " pdb=" C ILE C 645 " pdb=" CB ILE C 645 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 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 4.33e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 431 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 431 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 431 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 114 " 0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO A 115 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 94 " -0.017 5.00e-02 4.00e+02 2.63e-02 1.10e+00 pdb=" N PRO A 95 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.015 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 16 2.44 - 3.06: 3199 3.06 - 3.67: 6746 3.67 - 4.29: 10189 4.29 - 4.90: 17722 Nonbonded interactions: 37872 Sorted by model distance: nonbonded pdb=" SG CYS C 639 " pdb=" C03 A1AIV B 101 " model vdw 1.831 3.800 nonbonded pdb=" OE1 GLN B 2 " pdb=" OG1 THR B 14 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASN C 478 " pdb=" OG SER C 483 " model vdw 2.313 3.040 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.324 3.040 nonbonded pdb=" OE2 GLU A 9 " pdb=" OH TYR A 60 " model vdw 2.344 3.040 ... (remaining 37867 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=0.37 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: 1.810 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.320 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 0.073 4983 Z= 0.176 Angle : 0.471 5.255 6747 Z= 0.232 Chirality : 0.039 0.136 737 Planarity : 0.003 0.030 873 Dihedral : 10.222 66.463 1878 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.29 % Allowed : 6.08 % Favored : 92.63 % 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: 1.13 (0.37), residues: 594 helix: 1.70 (0.34), residues: 250 sheet: 0.68 (0.61), residues: 82 loop : -0.09 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS A 75 PHE 0.009 0.001 PHE C 522 TYR 0.007 0.001 TYR C 367 ARG 0.002 0.000 ARG C 422 *********************** 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 101 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 83 SER cc_start: 0.8825 (m) cc_final: 0.8602 (t) REVERT: B 42 ARG cc_start: 0.6175 (ttt90) cc_final: 0.5960 (ttt90) REVERT: C 613 MET cc_start: 0.8614 (ttt) cc_final: 0.8319 (ttt) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 0.2420 time to fit residues: 28.6676 Evaluate side-chains 61 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7805 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4983 Z= 0.310 Angle : 0.570 6.641 6747 Z= 0.291 Chirality : 0.043 0.164 737 Planarity : 0.004 0.034 873 Dihedral : 4.968 41.088 670 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.39 % Allowed : 10.13 % Favored : 87.48 % 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: 0.92 (0.37), residues: 594 helix: 1.58 (0.34), residues: 259 sheet: 0.46 (0.61), residues: 83 loop : -0.30 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.000 HIS A 55 PHE 0.019 0.002 PHE C 480 TYR 0.012 0.002 TYR C 419 ARG 0.007 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 76 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7421 (ttm-80) REVERT: A 83 SER cc_start: 0.8832 (m) cc_final: 0.8604 (t) REVERT: A 92 GLN cc_start: 0.7758 (mt0) cc_final: 0.7255 (mt0) REVERT: A 114 ASN cc_start: 0.7154 (t0) cc_final: 0.6843 (t0) REVERT: A 143 ARG cc_start: 0.8282 (tpm170) cc_final: 0.8022 (tpm170) REVERT: C 587 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.8117 (m-10) REVERT: C 613 MET cc_start: 0.8774 (ttt) cc_final: 0.8501 (ttt) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.2268 time to fit residues: 20.2991 Evaluate side-chains 68 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 LEU 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: 0.9980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 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: 0.7809 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 0.040 4983 Z= 0.290 Angle : 0.568 7.951 6747 Z= 0.288 Chirality : 0.044 0.252 737 Planarity : 0.005 0.065 873 Dihedral : 4.587 38.363 664 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.76 % Allowed : 11.60 % Favored : 85.64 % 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: 0.87 (0.37), residues: 594 helix: 1.59 (0.34), residues: 259 sheet: 0.51 (0.60), residues: 83 loop : -0.41 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.001 HIS A 55 PHE 0.012 0.002 PHE C 480 TYR 0.022 0.001 TYR A 145 ARG 0.006 0.001 ARG B 54 *********************** 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 74 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.8923 (m) cc_final: 0.8622 (t) REVERT: A 92 GLN cc_start: 0.7771 (mt0) cc_final: 0.7325 (mt0) REVERT: A 99 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7501 (tp) REVERT: A 114 ASN cc_start: 0.7130 (t0) cc_final: 0.6666 (t0) REVERT: B 43 LEU cc_start: 0.7873 (tt) cc_final: 0.7454 (mm) REVERT: C 349 ARG cc_start: 0.7428 (mtt180) cc_final: 0.7152 (mtm-85) REVERT: C 613 MET cc_start: 0.8856 (ttt) cc_final: 0.8610 (ttt) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.2203 time to fit residues: 19.0466 Evaluate side-chains 68 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 50 optimal weight: 0.0870 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 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: 0.7802 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4983 Z= 0.248 Angle : 0.533 7.866 6747 Z= 0.270 Chirality : 0.042 0.129 737 Planarity : 0.004 0.050 873 Dihedral : 4.562 37.934 664 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.95 % Allowed : 11.60 % Favored : 85.45 % 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: 0.90 (0.37), residues: 594 helix: 1.58 (0.34), residues: 260 sheet: 0.61 (0.61), residues: 81 loop : -0.40 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS A 55 PHE 0.009 0.001 PHE C 522 TYR 0.021 0.001 TYR A 145 ARG 0.008 0.001 ARG A 72 *********************** 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 75 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7276 (ttm-80) REVERT: A 83 SER cc_start: 0.8949 (m) cc_final: 0.8674 (t) REVERT: A 92 GLN cc_start: 0.7661 (mt0) cc_final: 0.7269 (mt0) REVERT: A 99 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7461 (tp) REVERT: A 114 ASN cc_start: 0.7096 (t0) cc_final: 0.6618 (t0) REVERT: A 145 TYR cc_start: 0.7910 (m-10) cc_final: 0.7597 (m-10) REVERT: C 613 MET cc_start: 0.8926 (ttt) cc_final: 0.8712 (ttt) outliers start: 16 outliers final: 12 residues processed: 73 average time/residue: 0.2259 time to fit residues: 20.3152 Evaluate side-chains 69 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7789 moved from start: 0.2090 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= 0.199 Angle : 0.525 8.424 6747 Z= 0.262 Chirality : 0.041 0.142 737 Planarity : 0.004 0.055 873 Dihedral : 4.522 38.035 664 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.58 % Allowed : 12.89 % Favored : 84.53 % 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 (0.37), residues: 594 helix: 1.61 (0.34), residues: 260 sheet: 0.70 (0.62), residues: 81 loop : -0.38 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.002 0.000 HIS A 55 PHE 0.008 0.001 PHE C 522 TYR 0.009 0.001 TYR C 419 ARG 0.005 0.000 ARG B 42 *********************** 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 72 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7334 (ttm-80) REVERT: A 83 SER cc_start: 0.8950 (m) cc_final: 0.8668 (t) REVERT: A 92 GLN cc_start: 0.7634 (mt0) cc_final: 0.7246 (mt0) REVERT: A 99 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7453 (tp) REVERT: A 114 ASN cc_start: 0.7113 (t0) cc_final: 0.6602 (t0) REVERT: A 128 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8396 (mmtt) REVERT: B 43 LEU cc_start: 0.7807 (tt) cc_final: 0.7343 (mm) REVERT: C 294 MET cc_start: 0.7148 (mmm) cc_final: 0.6799 (mmm) REVERT: C 349 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7154 (mtm-85) REVERT: C 613 MET cc_start: 0.8877 (ttt) cc_final: 0.8653 (ttt) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.2366 time to fit residues: 19.6024 Evaluate side-chains 69 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.0020 chunk 4 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 0.0030 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 overall best weight: 0.0914 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4983 Z= 0.114 Angle : 0.513 8.712 6747 Z= 0.253 Chirality : 0.039 0.134 737 Planarity : 0.004 0.045 873 Dihedral : 4.421 38.316 664 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.21 % Allowed : 13.26 % Favored : 84.53 % 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: 1.17 (0.37), residues: 594 helix: 1.84 (0.34), residues: 259 sheet: 0.77 (0.63), residues: 80 loop : -0.30 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.000 HIS C 512 PHE 0.007 0.001 PHE C 428 TYR 0.009 0.001 TYR A 127 ARG 0.013 0.001 ARG A 143 *********************** 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 72 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.8885 (m) cc_final: 0.8621 (t) REVERT: A 92 GLN cc_start: 0.7508 (mt0) cc_final: 0.7172 (mt0) REVERT: A 128 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8488 (mmtp) REVERT: A 145 TYR cc_start: 0.7884 (m-10) cc_final: 0.7575 (m-80) REVERT: B 43 LEU cc_start: 0.7764 (tt) cc_final: 0.7506 (mm) REVERT: C 613 MET cc_start: 0.8857 (ttt) cc_final: 0.8550 (ttp) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.2240 time to fit residues: 18.8261 Evaluate side-chains 68 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 318 GLN Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4983 Z= 0.182 Angle : 0.527 7.628 6747 Z= 0.262 Chirality : 0.040 0.129 737 Planarity : 0.004 0.045 873 Dihedral : 4.436 38.719 664 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.84 % Allowed : 13.81 % Favored : 84.35 % 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: 1.86 (0.34), residues: 258 sheet: 0.93 (0.63), residues: 81 loop : -0.30 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS A 55 PHE 0.008 0.001 PHE C 522 TYR 0.008 0.001 TYR C 419 ARG 0.008 0.001 ARG A 72 *********************** 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 68 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7229 (ttm-80) REVERT: A 83 SER cc_start: 0.8908 (m) cc_final: 0.8634 (t) REVERT: A 92 GLN cc_start: 0.7587 (mt0) cc_final: 0.7262 (mt0) REVERT: A 104 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7185 (tt) REVERT: B 43 LEU cc_start: 0.7693 (tt) cc_final: 0.7385 (mm) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.2199 time to fit residues: 18.1649 Evaluate side-chains 64 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4983 Z= 0.226 Angle : 0.551 7.963 6747 Z= 0.273 Chirality : 0.041 0.127 737 Planarity : 0.004 0.050 873 Dihedral : 4.506 38.639 664 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.21 % Allowed : 13.81 % Favored : 83.98 % 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: 1.18 (0.37), residues: 594 helix: 1.83 (0.34), residues: 258 sheet: 0.98 (0.64), residues: 81 loop : -0.33 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.001 0.000 HIS A 55 PHE 0.010 0.001 PHE C 522 TYR 0.010 0.001 TYR A 145 ARG 0.010 0.001 ARG A 143 *********************** 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 67 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7310 (ttm-80) REVERT: A 83 SER cc_start: 0.8966 (m) cc_final: 0.8669 (t) REVERT: A 92 GLN cc_start: 0.7520 (mt0) cc_final: 0.7255 (mt0) REVERT: A 104 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7191 (tt) REVERT: A 114 ASN cc_start: 0.7817 (t0) cc_final: 0.7201 (t0) REVERT: A 144 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7550 (tmmt) REVERT: B 43 LEU cc_start: 0.7750 (tt) cc_final: 0.7358 (mm) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.2134 time to fit residues: 16.7792 Evaluate side-chains 63 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0670 chunk 49 optimal weight: 0.0470 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4983 Z= 0.172 Angle : 0.547 8.388 6747 Z= 0.269 Chirality : 0.040 0.130 737 Planarity : 0.004 0.051 873 Dihedral : 4.500 38.381 664 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.84 % Allowed : 14.73 % Favored : 83.43 % 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: 1.23 (0.37), residues: 594 helix: 1.88 (0.34), residues: 258 sheet: 1.02 (0.65), residues: 81 loop : -0.32 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 93 HIS 0.001 0.000 HIS C 420 PHE 0.007 0.001 PHE C 522 TYR 0.012 0.001 TYR A 127 ARG 0.006 0.001 ARG A 72 *********************** 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 64 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7290 (ttm-80) REVERT: A 83 SER cc_start: 0.8964 (m) cc_final: 0.8671 (t) REVERT: A 92 GLN cc_start: 0.7455 (mt0) cc_final: 0.7191 (mt0) REVERT: A 104 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7185 (tt) REVERT: A 114 ASN cc_start: 0.7793 (t0) cc_final: 0.7235 (t0) REVERT: B 43 LEU cc_start: 0.7843 (tt) cc_final: 0.7311 (mm) REVERT: C 294 MET cc_start: 0.6930 (mmm) cc_final: 0.6564 (mmm) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.2170 time to fit residues: 16.9948 Evaluate side-chains 63 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 14 optimal weight: 0.0470 chunk 42 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.2876 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4983 Z= 0.156 Angle : 0.538 8.546 6747 Z= 0.267 Chirality : 0.040 0.130 737 Planarity : 0.004 0.054 873 Dihedral : 4.519 38.521 664 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.84 % Allowed : 14.92 % Favored : 83.24 % 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: 1.23 (0.37), residues: 594 helix: 1.84 (0.34), residues: 258 sheet: 0.96 (0.64), residues: 80 loop : -0.26 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS C 512 PHE 0.007 0.001 PHE C 407 TYR 0.011 0.001 TYR A 127 ARG 0.012 0.001 ARG A 143 ********************** 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 65 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7315 (ttm-80) REVERT: A 83 SER cc_start: 0.8964 (m) cc_final: 0.8652 (t) REVERT: A 92 GLN cc_start: 0.7448 (mt0) cc_final: 0.7161 (mt0) REVERT: A 114 ASN cc_start: 0.7751 (t0) cc_final: 0.7171 (t0) REVERT: A 144 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7966 (tmmt) REVERT: B 43 LEU cc_start: 0.7957 (tt) cc_final: 0.7407 (mm) REVERT: C 294 MET cc_start: 0.7045 (mmm) cc_final: 0.6662 (mmm) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.2153 time to fit residues: 16.6098 Evaluate side-chains 63 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0170 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.141648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092026 restraints weight = 17708.938| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 5.43 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4983 Z= 0.162 Angle : 0.538 8.572 6747 Z= 0.268 Chirality : 0.040 0.130 737 Planarity : 0.004 0.054 873 Dihedral : 4.509 38.506 664 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.21 % Allowed : 14.55 % Favored : 83.24 % 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: 1.27 (0.37), residues: 594 helix: 1.85 (0.34), residues: 258 sheet: 1.11 (0.65), residues: 78 loop : -0.25 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 93 HIS 0.001 0.000 HIS C 512 PHE 0.007 0.001 PHE C 522 TYR 0.010 0.001 TYR A 127 ARG 0.006 0.000 ARG A 72 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1479.65 seconds wall clock time: 26 minutes 52.26 seconds (1612.26 seconds total)