Starting phenix.real_space_refine on Fri Aug 2 20:05:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5b_44206/08_2024/9b5b_44206.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5b_44206/08_2024/9b5b_44206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5b_44206/08_2024/9b5b_44206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5b_44206/08_2024/9b5b_44206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5b_44206/08_2024/9b5b_44206.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5b_44206/08_2024/9b5b_44206.cif" } resolution = 3.31 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= 0.044 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: 0.02s 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: 5.08, per 1000 atoms: 1.04 Number of scatterers: 4871 At special positions: 0 Unit cell: (74.48, 82.992, 98.952, 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: 2.01 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: 27 helices and 6 sheets defined 48.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.690A pdb=" N VAL A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 307 through 311 removed outlier: 4.119A pdb=" N ALA C 311 " --> pdb=" O PRO C 308 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.489A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.516A pdb=" N TYR C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.807A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.552A 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 531 Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.579A 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 Processing helix chain 'C' and resid 588 through 601 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 663 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 Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321 removed outlier: 3.764A 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: 3.699A 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 568 228 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: 1.29 Time building geometry restraints manager: 2.09 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 - 1.40: 1233 1.40 - 1.54: 2853 1.54 - 1.67: 53 1.67 - 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 1.525 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.21e-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 4.11e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 100.51 - 116.36: 3314 116.36 - 132.21: 3424 132.21 - 148.06: 8 148.06 - 163.91: 0 163.91 - 179.75: 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 109.79 107.61 2.18 1.56e+00 4.11e-01 1.96e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 111.99 -2.65 2.08e+00 2.31e-01 1.63e+00 angle pdb=" N GLY B 75 " pdb=" CA GLY B 75 " pdb=" C GLY B 75 " ideal model delta sigma weight residual 113.30 109.74 3.56 2.90e+00 1.19e-01 1.51e+00 angle pdb=" C SER A 19 " pdb=" CA SER A 19 " pdb=" CB SER A 19 " ideal model delta sigma weight residual 110.65 108.56 2.09 1.95e+00 2.63e-01 1.15e+00 angle pdb=" N GLY A 82 " pdb=" CA GLY A 82 " pdb=" C GLY A 82 " ideal model delta sigma weight residual 114.95 113.49 1.46 1.41e+00 5.03e-01 1.08e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 2818 14.30 - 28.59: 166 28.59 - 42.89: 30 42.89 - 57.19: 2 57.19 - 71.48: 2 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: 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 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+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 -81.35 51.35 1 2.00e+01 2.50e-03 9.01e+00 dihedral pdb=" N LEU C 509 " pdb=" CA LEU C 509 " pdb=" CB LEU C 509 " pdb=" CG LEU C 509 " ideal model delta sinusoidal sigma weight residual -60.00 -103.44 43.44 3 1.50e+01 4.44e-03 7.81e+00 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 450 0.028 - 0.056: 192 0.056 - 0.084: 51 0.084 - 0.112: 30 0.112 - 0.140: 14 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 4.90e-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 4.54e-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 4.06e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 76 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO C 431 " -0.051 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 SER A 94 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.18e-01 pdb=" N PRO A 95 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.013 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 6 2.41 - 3.03: 2955 3.03 - 3.65: 6690 3.65 - 4.28: 10351 4.28 - 4.90: 17782 Nonbonded interactions: 37784 Sorted by model distance: nonbonded pdb=" SG CYS C 639 " pdb=" C03 A1AIV B 101 " model vdw 1.782 3.800 nonbonded pdb=" OG SER C 397 " pdb=" OE1 GLN C 521 " model vdw 2.333 3.040 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.341 3.040 nonbonded pdb=" OE2 GLU A 9 " pdb=" OH TYR A 60 " model vdw 2.380 3.040 nonbonded pdb=" ND2 ASN C 478 " pdb=" O GLY C 481 " model vdw 2.392 3.120 ... (remaining 37779 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=0.34 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: 2.200 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4983 Z= 0.203 Angle : 0.435 3.846 6747 Z= 0.217 Chirality : 0.039 0.140 737 Planarity : 0.003 0.034 873 Dihedral : 9.362 71.483 1878 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.29 % Allowed : 3.87 % Favored : 94.84 % 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: 1.85 (0.37), residues: 594 helix: 2.12 (0.34), residues: 252 sheet: 1.04 (0.56), residues: 97 loop : 0.47 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS C 420 PHE 0.009 0.001 PHE C 580 TYR 0.009 0.001 TYR C 367 ARG 0.002 0.000 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7737 (pt0) cc_final: 0.7533 (tt0) REVERT: A 66 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8160 (tttm) REVERT: A 87 ASP cc_start: 0.8764 (p0) cc_final: 0.8335 (p0) REVERT: A 91 ASP cc_start: 0.8054 (t0) cc_final: 0.7420 (t0) REVERT: A 114 ASN cc_start: 0.7940 (t0) cc_final: 0.6212 (t0) REVERT: A 130 ASP cc_start: 0.7058 (t0) cc_final: 0.6337 (t0) REVERT: A 140 GLU cc_start: 0.8771 (mm-30) cc_final: 0.7906 (mm-30) REVERT: B 1 MET cc_start: 0.1932 (ptt) cc_final: 0.1383 (ptt) REVERT: C 554 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8234 (ttm-80) REVERT: C 640 PHE cc_start: 0.8417 (t80) cc_final: 0.8206 (t80) outliers start: 7 outliers final: 2 residues processed: 99 average time/residue: 0.2671 time to fit residues: 31.6937 Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.7942 moved from start: 0.1542 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= 0.235 Angle : 0.538 6.562 6747 Z= 0.273 Chirality : 0.041 0.133 737 Planarity : 0.004 0.034 873 Dihedral : 4.705 47.419 664 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.29 % Allowed : 9.02 % Favored : 89.69 % 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: 1.79 (0.37), residues: 594 helix: 2.07 (0.34), residues: 253 sheet: 1.01 (0.56), residues: 97 loop : 0.41 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.011 0.001 PHE C 522 TYR 0.010 0.001 TYR A 145 ARG 0.006 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7770 (pt0) cc_final: 0.7518 (tt0) REVERT: A 66 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8091 (tttm) REVERT: A 72 ARG cc_start: 0.8266 (mtp85) cc_final: 0.8049 (mtp85) REVERT: A 91 ASP cc_start: 0.8213 (t0) cc_final: 0.7916 (t0) REVERT: A 140 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8200 (mm-30) REVERT: C 554 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8218 (ttm-80) outliers start: 7 outliers final: 7 residues processed: 68 average time/residue: 0.2088 time to fit residues: 17.8207 Evaluate side-chains 56 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 399 VAL 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: 0.4980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 42 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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: 0.7934 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4983 Z= 0.186 Angle : 0.502 7.181 6747 Z= 0.254 Chirality : 0.040 0.131 737 Planarity : 0.004 0.036 873 Dihedral : 4.658 49.741 664 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.66 % Allowed : 9.94 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.37), residues: 594 helix: 2.13 (0.34), residues: 255 sheet: 1.19 (0.57), residues: 95 loop : 0.53 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR A 145 ARG 0.005 0.000 ARG C 349 *********************** 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: 9 poor density : 51 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7759 (pt0) cc_final: 0.7539 (tt0) REVERT: A 66 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8084 (tttm) REVERT: A 91 ASP cc_start: 0.8190 (t0) cc_final: 0.7847 (t0) REVERT: A 140 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8222 (mm-30) REVERT: C 554 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8255 (ttm-80) outliers start: 9 outliers final: 9 residues processed: 56 average time/residue: 0.2469 time to fit residues: 17.0164 Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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: 0.7943 moved from start: 0.1857 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 : 0.501 6.960 6747 Z= 0.254 Chirality : 0.040 0.164 737 Planarity : 0.004 0.050 873 Dihedral : 4.701 50.052 664 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.58 % Allowed : 9.94 % 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: 1.95 (0.37), residues: 594 helix: 2.19 (0.34), residues: 255 sheet: 1.16 (0.57), residues: 95 loop : 0.49 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.011 0.001 PHE C 522 TYR 0.009 0.001 TYR A 145 ARG 0.006 0.000 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 71 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7310 (t0) cc_final: 0.7072 (t0) REVERT: A 34 GLN cc_start: 0.7785 (pt0) cc_final: 0.7513 (tt0) REVERT: A 66 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8099 (tttm) REVERT: A 91 ASP cc_start: 0.8068 (t0) cc_final: 0.7789 (t0) REVERT: A 140 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8256 (mm-30) outliers start: 14 outliers final: 12 residues processed: 66 average time/residue: 0.2123 time to fit residues: 17.6663 Evaluate side-chains 56 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE 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: 0.2980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4983 Z= 0.255 Angle : 0.514 6.847 6747 Z= 0.260 Chirality : 0.041 0.161 737 Planarity : 0.004 0.038 873 Dihedral : 4.751 50.069 664 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.21 % Allowed : 10.68 % Favored : 87.11 % 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: 1.93 (0.37), residues: 594 helix: 2.21 (0.34), residues: 253 sheet: 1.16 (0.58), residues: 95 loop : 0.45 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.013 0.001 PHE C 522 TYR 0.008 0.001 TYR C 419 ARG 0.004 0.000 ARG C 349 *********************** 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 62 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8113 (tttm) REVERT: A 72 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8074 (mtp85) REVERT: A 81 ASN cc_start: 0.8841 (m110) cc_final: 0.8569 (m110) REVERT: A 91 ASP cc_start: 0.8043 (t0) cc_final: 0.7819 (t0) REVERT: A 140 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8213 (mm-30) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.2347 time to fit residues: 16.2776 Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.2012 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= 0.236 Angle : 0.509 7.282 6747 Z= 0.259 Chirality : 0.041 0.151 737 Planarity : 0.004 0.039 873 Dihedral : 4.786 50.875 664 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.58 % Allowed : 10.87 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.37), residues: 594 helix: 2.19 (0.34), residues: 253 sheet: 1.17 (0.58), residues: 95 loop : 0.44 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.011 0.001 PHE C 522 TYR 0.009 0.001 TYR C 419 ARG 0.008 0.001 ARG A 139 *********************** 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 63 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8110 (tttm) REVERT: A 72 ARG cc_start: 0.8386 (mtp85) cc_final: 0.8078 (mtp85) REVERT: A 91 ASP cc_start: 0.8036 (t0) cc_final: 0.7799 (t0) REVERT: A 140 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 143 ARG cc_start: 0.8786 (tmm-80) cc_final: 0.8048 (tmm-80) REVERT: C 640 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7493 (m-80) outliers start: 14 outliers final: 11 residues processed: 57 average time/residue: 0.2244 time to fit residues: 16.6767 Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE 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: 0.7980 chunk 55 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.2040 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= 0.166 Angle : 0.481 7.738 6747 Z= 0.245 Chirality : 0.040 0.152 737 Planarity : 0.004 0.037 873 Dihedral : 4.684 51.102 664 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.21 % Allowed : 10.87 % Favored : 86.92 % 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: 2.02 (0.37), residues: 594 helix: 2.28 (0.34), residues: 253 sheet: 1.21 (0.58), residues: 95 loop : 0.49 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.007 0.001 PHE C 522 TYR 0.007 0.001 TYR C 419 ARG 0.005 0.000 ARG A 139 *********************** 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 62 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8103 (tttm) REVERT: A 72 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8063 (mtp85) REVERT: A 91 ASP cc_start: 0.8030 (t0) cc_final: 0.7787 (t0) REVERT: A 140 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8170 (mm-30) REVERT: A 143 ARG cc_start: 0.8685 (tmm-80) cc_final: 0.8008 (tmm-80) REVERT: C 640 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7521 (m-80) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.2280 time to fit residues: 16.2156 Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.0270 chunk 22 optimal weight: 0.0770 chunk 40 optimal weight: 0.0570 chunk 15 optimal weight: 8.9990 overall best weight: 0.1752 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4983 Z= 0.135 Angle : 0.471 8.151 6747 Z= 0.239 Chirality : 0.039 0.151 737 Planarity : 0.004 0.048 873 Dihedral : 4.578 51.741 664 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.84 % Allowed : 11.23 % Favored : 86.92 % 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: 2.17 (0.38), residues: 594 helix: 2.39 (0.34), residues: 254 sheet: 1.29 (0.57), residues: 95 loop : 0.57 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 459 HIS 0.001 0.000 HIS C 420 PHE 0.006 0.001 PHE C 407 TYR 0.006 0.001 TYR C 419 ARG 0.005 0.000 ARG A 139 *********************** 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 60 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8090 (tttm) REVERT: A 91 ASP cc_start: 0.8021 (t0) cc_final: 0.7791 (t0) REVERT: A 140 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8135 (mm-30) REVERT: A 143 ARG cc_start: 0.8703 (tmm-80) cc_final: 0.8046 (tmm-80) REVERT: C 425 ASP cc_start: 0.7652 (m-30) cc_final: 0.7373 (m-30) REVERT: C 640 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7554 (m-80) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.2051 time to fit residues: 14.5803 Evaluate side-chains 56 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4983 Z= 0.233 Angle : 0.510 8.857 6747 Z= 0.258 Chirality : 0.040 0.146 737 Planarity : 0.004 0.041 873 Dihedral : 4.395 51.897 662 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.21 % Allowed : 10.87 % Favored : 86.92 % 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: 2.09 (0.38), residues: 594 helix: 2.30 (0.34), residues: 254 sheet: 1.28 (0.58), residues: 95 loop : 0.55 (0.46), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.012 0.001 PHE C 522 TYR 0.008 0.001 TYR C 419 ARG 0.005 0.000 ARG B 74 *********************** 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 59 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8094 (tttm) REVERT: A 91 ASP cc_start: 0.8039 (t0) cc_final: 0.7525 (t0) REVERT: A 140 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8243 (mm-30) REVERT: A 143 ARG cc_start: 0.8731 (tmm-80) cc_final: 0.8102 (tmm-80) REVERT: C 640 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7575 (m-80) outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 0.2220 time to fit residues: 15.1623 Evaluate side-chains 55 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.0980 chunk 35 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.0770 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.0030 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 overall best weight: 0.1948 ------------------------------------------------------------------------------- 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: 0.7921 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4983 Z= 0.145 Angle : 0.500 9.602 6747 Z= 0.254 Chirality : 0.039 0.150 737 Planarity : 0.004 0.036 873 Dihedral : 4.330 52.084 662 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.47 % Allowed : 11.60 % Favored : 86.92 % 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: 2.20 (0.38), residues: 594 helix: 2.39 (0.34), residues: 254 sheet: 1.37 (0.58), residues: 95 loop : 0.59 (0.46), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.002 0.000 HIS C 420 PHE 0.007 0.001 PHE C 428 TYR 0.007 0.001 TYR C 419 ARG 0.004 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8081 (tttm) REVERT: A 72 ARG cc_start: 0.8357 (mtp85) cc_final: 0.8066 (mtp85) REVERT: A 81 ASN cc_start: 0.8726 (m110) cc_final: 0.8459 (m110) REVERT: A 91 ASP cc_start: 0.8175 (t0) cc_final: 0.7798 (t0) REVERT: A 92 GLN cc_start: 0.8485 (mp10) cc_final: 0.7899 (mp10) REVERT: A 140 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8201 (mm-30) REVERT: A 143 ARG cc_start: 0.8697 (tmm-80) cc_final: 0.8051 (tmm-80) REVERT: C 425 ASP cc_start: 0.7523 (m-30) cc_final: 0.7310 (m-30) REVERT: C 640 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7605 (m-80) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.2113 time to fit residues: 14.2041 Evaluate side-chains 61 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.133759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.082225 restraints weight = 17957.020| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 5.15 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2229 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= 0.275 Angle : 0.534 10.844 6747 Z= 0.268 Chirality : 0.041 0.146 737 Planarity : 0.004 0.039 873 Dihedral : 4.448 51.936 662 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 11.60 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.38), residues: 594 helix: 2.29 (0.34), residues: 254 sheet: 1.32 (0.59), residues: 95 loop : 0.56 (0.46), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.014 0.001 PHE C 522 TYR 0.009 0.001 TYR C 419 ARG 0.004 0.000 ARG B 74 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1505.57 seconds wall clock time: 27 minutes 22.23 seconds (1642.23 seconds total)