Starting phenix.real_space_refine on Fri Aug 2 20:06:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b58_44203/08_2024/9b58_44203.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b58_44203/08_2024/9b58_44203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b58_44203/08_2024/9b58_44203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b58_44203/08_2024/9b58_44203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b58_44203/08_2024/9b58_44203.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b58_44203/08_2024/9b58_44203.cif" } resolution = 3.39 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= 0.041 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 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: 5.00, per 1000 atoms: 1.03 Number of scatterers: 4871 At special positions: 0 Unit cell: (69.16, 82.992, 101.08, 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: 1.93 Conformation dependent library (CDL) restraints added in 1.6 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 50.3% alpha, 12.2% 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 86 through 91 Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.094A 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 307 through 311 removed outlier: 4.057A pdb=" N ALA C 311 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.518A pdb=" N SER C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 357 through 374 removed outlier: 3.518A pdb=" N PHE C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.582A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.395A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.567A 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: 3.857A 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: 3.820A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.671A 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 518 through 533 removed outlier: 4.284A pdb=" N LEU C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) 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: 3.937A 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: 3.591A 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: 3.885A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321 removed outlier: 3.703A 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 385 removed outlier: 6.764A pdb=" N GLY C 390 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 474 through 479 Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568 224 hydrogen bonds defined for protein. 626 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: 2.13 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: 1234 1.41 - 1.54: 2889 1.54 - 1.68: 16 1.68 - 1.81: 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 1.527 -0.074 2.00e-02 2.50e+03 1.36e+01 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 2.75e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 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 1.133 0.018 2.00e-02 2.50e+03 8.00e-01 bond pdb=" CG LEU C 595 " pdb=" CD2 LEU C 595 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.21e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 100.58 - 116.33: 3304 116.33 - 132.09: 3434 132.09 - 147.84: 8 147.84 - 163.60: 0 163.60 - 179.35: 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 110.35 108.22 2.13 1.38e+00 5.25e-01 2.39e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 111.91 -2.57 2.08e+00 2.31e-01 1.52e+00 angle pdb=" CA TRP C 561 " pdb=" CB TRP C 561 " pdb=" CG TRP C 561 " ideal model delta sigma weight residual 113.60 115.65 -2.05 1.90e+00 2.77e-01 1.16e+00 angle pdb=" C LEU A 89 " pdb=" N ARG A 90 " pdb=" CA ARG A 90 " ideal model delta sigma weight residual 121.54 119.51 2.03 1.91e+00 2.74e-01 1.13e+00 angle pdb=" N SER C 569 " pdb=" CA SER C 569 " pdb=" CB SER C 569 " ideal model delta sigma weight residual 112.78 111.20 1.58 1.53e+00 4.27e-01 1.06e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 2802 15.54 - 31.07: 186 31.07 - 46.61: 24 46.61 - 62.15: 4 62.15 - 77.68: 2 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA TYR A 145 " pdb=" C TYR A 145 " pdb=" N ALA A 146 " pdb=" CA ALA A 146 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 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 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU A 119 " pdb=" C LEU A 119 " pdb=" N VAL A 120 " pdb=" CA VAL A 120 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 441 0.028 - 0.055: 197 0.055 - 0.082: 57 0.082 - 0.110: 27 0.110 - 0.137: 15 Chirality restraints: 737 Sorted by residual: 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 2.57 -0.14 2.00e-01 2.50e+01 4.72e-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 -0.14 2.00e-01 2.50e+01 4.62e-01 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 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 117 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 118 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 431 " -0.052 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 PRO C 646 " -0.018 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO C 647 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 647 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 647 " -0.016 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 16 2.43 - 3.05: 3104 3.05 - 3.66: 6734 3.66 - 4.28: 10344 4.28 - 4.90: 17704 Nonbonded interactions: 37902 Sorted by model distance: nonbonded pdb=" SG CYS C 639 " pdb=" C03 A1AIV B 101 " model vdw 1.812 3.800 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 29 " model vdw 2.221 3.120 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.303 3.040 nonbonded pdb=" OG SER C 397 " pdb=" OE1 GLN C 521 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASN C 478 " pdb=" OG SER C 483 " model vdw 2.316 3.040 ... (remaining 37897 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=0.39 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.560 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 0.074 4983 Z= 0.158 Angle : 0.453 3.898 6747 Z= 0.226 Chirality : 0.039 0.137 737 Planarity : 0.003 0.033 873 Dihedral : 10.328 77.683 1878 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.10 % Allowed : 6.08 % Favored : 92.82 % 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: 0.81 (0.37), residues: 594 helix: 1.28 (0.33), residues: 257 sheet: 0.66 (0.61), residues: 85 loop : -0.19 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS A 125 PHE 0.009 0.001 PHE C 407 TYR 0.010 0.001 TYR C 367 ARG 0.002 0.000 ARG C 404 *********************** 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 75 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7679 (ttt90) REVERT: C 318 GLN cc_start: 0.8449 (pt0) cc_final: 0.8232 (pm20) REVERT: C 347 LEU cc_start: 0.8076 (tp) cc_final: 0.7834 (mt) outliers start: 6 outliers final: 2 residues processed: 73 average time/residue: 0.2884 time to fit residues: 25.1417 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain C residue 385 THR 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: 0.8980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 52 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: 0.7840 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4983 Z= 0.286 Angle : 0.566 8.487 6747 Z= 0.291 Chirality : 0.042 0.155 737 Planarity : 0.004 0.044 873 Dihedral : 4.535 41.466 663 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.66 % Allowed : 10.68 % 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: 0.65 (0.36), residues: 594 helix: 1.10 (0.33), residues: 262 sheet: 0.76 (0.61), residues: 82 loop : -0.30 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 PHE 0.015 0.001 PHE C 564 TYR 0.010 0.001 TYR C 419 ARG 0.009 0.001 ARG C 568 *********************** 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 65 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7770 (ttt90) REVERT: C 347 LEU cc_start: 0.7991 (tp) cc_final: 0.7719 (mt) REVERT: C 572 GLU cc_start: 0.7820 (tp30) cc_final: 0.7458 (tp30) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.2187 time to fit residues: 16.8381 Evaluate side-chains 55 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 627 VAL 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: 0.9980 chunk 43 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 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: 0.7854 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4983 Z= 0.298 Angle : 0.554 9.685 6747 Z= 0.283 Chirality : 0.042 0.129 737 Planarity : 0.004 0.035 873 Dihedral : 4.517 39.017 663 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.21 % Allowed : 11.42 % 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: 0.65 (0.36), residues: 594 helix: 1.12 (0.33), residues: 260 sheet: 0.78 (0.61), residues: 82 loop : -0.34 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 PHE 0.011 0.001 PHE C 564 TYR 0.010 0.001 TYR C 419 ARG 0.006 0.000 ARG C 568 *********************** 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 60 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4514 (tmm) cc_final: 0.4081 (tmm) REVERT: C 347 LEU cc_start: 0.8090 (tp) cc_final: 0.7793 (mt) outliers start: 12 outliers final: 9 residues processed: 54 average time/residue: 0.2254 time to fit residues: 15.3030 Evaluate side-chains 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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: 0.7834 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4983 Z= 0.207 Angle : 0.525 7.598 6747 Z= 0.269 Chirality : 0.041 0.148 737 Planarity : 0.004 0.035 873 Dihedral : 4.388 34.819 663 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.31 % Allowed : 10.50 % 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: 0.76 (0.36), residues: 594 helix: 1.18 (0.33), residues: 260 sheet: 0.87 (0.61), residues: 82 loop : -0.26 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.001 0.000 HIS C 420 PHE 0.011 0.001 PHE C 428 TYR 0.014 0.001 TYR A 145 ARG 0.005 0.000 ARG C 412 *********************** 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 63 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7807 (tp) REVERT: B 1 MET cc_start: 0.5196 (tmm) cc_final: 0.4870 (tmm) REVERT: B 74 ARG cc_start: 0.7001 (mtp85) cc_final: 0.6393 (ttm110) REVERT: C 347 LEU cc_start: 0.8119 (tp) cc_final: 0.7821 (mt) REVERT: C 612 ASP cc_start: 0.9390 (OUTLIER) cc_final: 0.9032 (p0) outliers start: 18 outliers final: 11 residues processed: 57 average time/residue: 0.2221 time to fit residues: 15.9754 Evaluate side-chains 56 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4983 Z= 0.284 Angle : 0.538 7.122 6747 Z= 0.277 Chirality : 0.042 0.129 737 Planarity : 0.004 0.036 873 Dihedral : 4.459 35.537 663 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.95 % Allowed : 11.79 % Favored : 85.27 % 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: 0.66 (0.36), residues: 594 helix: 1.13 (0.33), residues: 260 sheet: 0.87 (0.61), residues: 82 loop : -0.36 (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 C 420 PHE 0.010 0.001 PHE C 598 TYR 0.017 0.001 TYR A 74 ARG 0.006 0.000 ARG C 412 *********************** 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 60 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7862 (tp) REVERT: B 1 MET cc_start: 0.5384 (tmm) cc_final: 0.4655 (tmm) REVERT: B 74 ARG cc_start: 0.7048 (mtp85) cc_final: 0.6442 (ttm110) REVERT: C 310 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8640 (ttm) REVERT: C 347 LEU cc_start: 0.8165 (tp) cc_final: 0.7838 (mt) REVERT: C 612 ASP cc_start: 0.9396 (OUTLIER) cc_final: 0.9062 (p0) outliers start: 16 outliers final: 11 residues processed: 54 average time/residue: 0.2149 time to fit residues: 14.6632 Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7851 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4983 Z= 0.242 Angle : 0.505 7.454 6747 Z= 0.262 Chirality : 0.041 0.129 737 Planarity : 0.004 0.036 873 Dihedral : 4.408 34.743 663 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.13 % Allowed : 11.42 % 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: 0.71 (0.36), residues: 594 helix: 1.18 (0.33), residues: 260 sheet: 0.92 (0.60), residues: 81 loop : -0.36 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 PHE 0.009 0.001 PHE C 428 TYR 0.015 0.001 TYR A 145 ARG 0.007 0.000 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 62 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 1 MET cc_start: 0.5426 (tmm) cc_final: 0.4622 (tmm) REVERT: B 74 ARG cc_start: 0.7058 (mtp85) cc_final: 0.6455 (ttm110) REVERT: C 310 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8611 (ttm) REVERT: C 347 LEU cc_start: 0.8166 (tp) cc_final: 0.7835 (mt) REVERT: C 612 ASP cc_start: 0.9389 (OUTLIER) cc_final: 0.9090 (p0) outliers start: 17 outliers final: 12 residues processed: 55 average time/residue: 0.2403 time to fit residues: 16.8049 Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.1993 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= 0.204 Angle : 0.540 14.714 6747 Z= 0.272 Chirality : 0.041 0.166 737 Planarity : 0.004 0.036 873 Dihedral : 4.349 32.470 663 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.13 % Allowed : 11.42 % 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: 0.74 (0.36), residues: 594 helix: 1.16 (0.33), residues: 264 sheet: 0.97 (0.60), residues: 81 loop : -0.30 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 141 HIS 0.002 0.000 HIS B 68 PHE 0.010 0.001 PHE C 564 TYR 0.017 0.001 TYR A 74 ARG 0.003 0.000 ARG C 412 *********************** 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 64 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 1 MET cc_start: 0.5673 (tmm) cc_final: 0.4771 (tmm) REVERT: B 74 ARG cc_start: 0.7151 (mtp85) cc_final: 0.6643 (ttm110) REVERT: C 310 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8589 (ttm) REVERT: C 347 LEU cc_start: 0.8163 (tp) cc_final: 0.7839 (mt) REVERT: C 612 ASP cc_start: 0.9375 (OUTLIER) cc_final: 0.9058 (p0) outliers start: 17 outliers final: 13 residues processed: 57 average time/residue: 0.2206 time to fit residues: 15.7320 Evaluate side-chains 61 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 627 VAL 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: 1.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 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: 0.7841 moved from start: 0.2066 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= 0.214 Angle : 0.526 12.172 6747 Z= 0.267 Chirality : 0.041 0.171 737 Planarity : 0.004 0.036 873 Dihedral : 4.273 31.564 663 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.95 % Allowed : 12.15 % Favored : 84.90 % 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: 0.70 (0.36), residues: 594 helix: 1.14 (0.33), residues: 264 sheet: 0.91 (0.59), residues: 81 loop : -0.34 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 141 HIS 0.001 0.001 HIS B 68 PHE 0.010 0.001 PHE C 564 TYR 0.009 0.001 TYR A 145 ARG 0.007 0.000 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 61 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.607 Fit side-chains REVERT: A 99 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7821 (tp) REVERT: B 1 MET cc_start: 0.5696 (tmm) cc_final: 0.4813 (tmm) REVERT: B 74 ARG cc_start: 0.7168 (mtp85) cc_final: 0.6166 (mtt180) REVERT: C 310 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8592 (ttm) REVERT: C 347 LEU cc_start: 0.8171 (tp) cc_final: 0.7841 (mt) REVERT: C 612 ASP cc_start: 0.9375 (OUTLIER) cc_final: 0.9000 (p0) outliers start: 16 outliers final: 11 residues processed: 54 average time/residue: 0.2264 time to fit residues: 15.3520 Evaluate side-chains 59 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4983 Z= 0.188 Angle : 0.536 11.550 6747 Z= 0.275 Chirality : 0.041 0.167 737 Planarity : 0.004 0.036 873 Dihedral : 4.219 29.048 663 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.76 % Allowed : 12.52 % Favored : 84.71 % 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: 0.61 (0.36), residues: 594 helix: 1.08 (0.33), residues: 265 sheet: 0.83 (0.61), residues: 75 loop : -0.36 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A 141 HIS 0.002 0.001 HIS B 68 PHE 0.009 0.001 PHE C 564 TYR 0.014 0.001 TYR A 74 ARG 0.008 0.001 ARG A 133 *********************** 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 61 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.538 Fit side-chains REVERT: A 99 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.7795 (tp) REVERT: B 1 MET cc_start: 0.5679 (tmm) cc_final: 0.4735 (tmm) REVERT: B 74 ARG cc_start: 0.7190 (mtp85) cc_final: 0.6622 (ttm110) REVERT: C 310 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8534 (ttm) REVERT: C 347 LEU cc_start: 0.8163 (tp) cc_final: 0.7835 (mt) REVERT: C 612 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.8999 (p0) outliers start: 15 outliers final: 11 residues processed: 56 average time/residue: 0.2234 time to fit residues: 15.5739 Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.0010 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 12 optimal weight: 0.0170 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 0.1222 ------------------------------------------------------------------------------- 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: 0.7787 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4983 Z= 0.131 Angle : 0.527 11.685 6747 Z= 0.274 Chirality : 0.040 0.196 737 Planarity : 0.004 0.037 873 Dihedral : 4.054 24.814 663 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.03 % Allowed : 13.44 % 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: 0.80 (0.36), residues: 594 helix: 1.21 (0.33), residues: 265 sheet: 0.94 (0.61), residues: 75 loop : -0.25 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP A 141 HIS 0.002 0.001 HIS A 125 PHE 0.023 0.001 PHE C 327 TYR 0.012 0.001 TYR A 74 ARG 0.008 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 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.572 Fit side-chains REVERT: B 1 MET cc_start: 0.5590 (tmm) cc_final: 0.4599 (tmm) REVERT: B 74 ARG cc_start: 0.7257 (mtp85) cc_final: 0.6281 (mtt180) REVERT: C 347 LEU cc_start: 0.8153 (tp) cc_final: 0.7825 (mt) REVERT: C 612 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.8963 (p0) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 0.2376 time to fit residues: 15.6069 Evaluate side-chains 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.146510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112525 restraints weight = 16771.173| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 5.32 r_work: 0.3200 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4983 Z= 0.243 Angle : 0.577 11.443 6747 Z= 0.300 Chirality : 0.044 0.234 737 Planarity : 0.004 0.042 873 Dihedral : 4.197 27.117 663 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.84 % Allowed : 13.63 % 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: 0.57 (0.36), residues: 594 helix: 1.01 (0.33), residues: 265 sheet: 0.89 (0.61), residues: 75 loop : -0.36 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.004 TRP A 141 HIS 0.003 0.001 HIS A 75 PHE 0.018 0.001 PHE C 327 TYR 0.014 0.001 TYR A 74 ARG 0.008 0.001 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1466.19 seconds wall clock time: 26 minutes 42.99 seconds (1602.99 seconds total)