Starting phenix.real_space_refine on Fri Aug 2 20:06:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b55_44200/08_2024/9b55_44200.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b55_44200/08_2024/9b55_44200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b55_44200/08_2024/9b55_44200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b55_44200/08_2024/9b55_44200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b55_44200/08_2024/9b55_44200.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b55_44200/08_2024/9b55_44200.cif" } resolution = 3.23 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 3110 2.51 5 N 824 2.21 5 O 923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 3107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} Conformer: "B" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} bond proxies already assigned to first conformer: 3161 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 1.05 Number of scatterers: 4871 At special positions: 0 Unit cell: (59.584, 81.928, 105.336, 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: 1.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 48.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.999A 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 145 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 357 through 374 Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.585A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.332A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.753A 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: 3.840A 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: 3.713A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 518 through 531 Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.649A pdb=" N LEU C 538 " --> pdb=" O PRO C 534 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 539 " --> pdb=" O ASP C 535 " (cutoff:3.500A) No H-bonds generated for '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: 3.948A pdb=" N PHE C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) 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 662 removed outlier: 3.706A 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: 4.145A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 321 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 474 through 479 removed outlier: 3.734A 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 568 222 hydrogen bonds defined for protein. 623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 820 1.27 - 1.41: 1241 1.41 - 1.54: 2896 1.54 - 1.68: 2 1.68 - 1.82: 24 Bond restraints: 4983 Sorted by residual: bond pdb=" C04 A1AIV B 101 " pdb=" C05 A1AIV B 101 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.30e+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 3.08e+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 2.79e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CA VAL A 120 " pdb=" CB VAL A 120 " ideal model delta sigma weight residual 1.540 1.534 0.006 9.00e-03 1.23e+04 4.25e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 100.24 - 116.07: 3269 116.07 - 131.91: 3469 131.91 - 147.74: 8 147.74 - 163.58: 0 163.58 - 179.42: 1 Bond angle restraints: 6747 Sorted by residual: angle pdb=" N LEU A 89 " pdb=" CA LEU A 89 " pdb=" C LEU A 89 " ideal model delta sigma weight residual 108.24 105.14 3.10 1.32e+00 5.74e-01 5.51e+00 angle pdb=" C ILE A 88 " pdb=" N LEU A 89 " pdb=" CA LEU A 89 " ideal model delta sigma weight residual 122.32 125.55 -3.23 1.76e+00 3.23e-01 3.36e+00 angle pdb=" N ILE A 88 " pdb=" CA ILE A 88 " pdb=" C ILE A 88 " ideal model delta sigma weight residual 111.58 109.70 1.88 1.06e+00 8.90e-01 3.16e+00 angle pdb=" CA VAL A 120 " pdb=" C VAL A 120 " pdb=" O VAL A 120 " ideal model delta sigma weight residual 120.88 119.68 1.20 6.80e-01 2.16e+00 3.12e+00 angle pdb=" N HIS B 68 " pdb=" CA HIS B 68 " pdb=" C HIS B 68 " ideal model delta sigma weight residual 108.90 111.76 -2.86 1.63e+00 3.76e-01 3.07e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 2769 13.01 - 26.02: 199 26.02 - 39.03: 38 39.03 - 52.04: 11 52.04 - 65.05: 1 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA ASP A 87 " pdb=" C ASP A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA LEU B 69 " pdb=" C LEU B 69 " pdb=" N VAL B 70 " pdb=" CA VAL B 70 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA VAL C 515 " pdb=" C VAL C 515 " pdb=" N THR C 516 " pdb=" CA THR C 516 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 438 0.028 - 0.056: 205 0.056 - 0.084: 49 0.084 - 0.112: 30 0.112 - 0.140: 15 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE B 36 " pdb=" N ILE B 36 " pdb=" C ILE B 36 " pdb=" CB ILE B 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-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 4.67e-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 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 67 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU B 67 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU B 67 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS B 68 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.08e-01 pdb=" N PRO A 76 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 5 " -0.005 2.00e-02 2.50e+03 9.50e-03 9.02e-01 pdb=" C VAL B 5 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL B 5 " -0.006 2.00e-02 2.50e+03 pdb=" N LYS B 6 " -0.006 2.00e-02 2.50e+03 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 11 2.45 - 3.06: 3323 3.06 - 3.67: 6653 3.67 - 4.29: 10184 4.29 - 4.90: 17785 Nonbonded interactions: 37956 Sorted by model distance: nonbonded pdb=" SG CYS A 85 " pdb=" C03 A1AIV B 101 " model vdw 1.834 3.800 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 29 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP C 555 " pdb=" N ILE C 556 " model vdw 2.240 3.120 nonbonded pdb=" N GLU C 664 " pdb=" OE1 GLU C 664 " model vdw 2.300 3.120 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.304 3.040 ... (remaining 37951 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=0.45 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: 2.160 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: 20.070 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.004 0.072 4983 Z= 0.275 Angle : 0.505 5.004 6747 Z= 0.274 Chirality : 0.040 0.140 737 Planarity : 0.003 0.024 873 Dihedral : 9.785 65.045 1878 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.35), residues: 594 helix: 1.85 (0.35), residues: 242 sheet: 0.58 (0.57), residues: 80 loop : -0.66 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.003 0.001 HIS A 75 PHE 0.009 0.001 PHE C 407 TYR 0.008 0.001 TYR C 453 ARG 0.001 0.000 ARG B 42 *********************** 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 61 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8718 (m-30) cc_final: 0.8390 (m-30) REVERT: A 114 ASN cc_start: 0.8851 (t0) cc_final: 0.8519 (t0) REVERT: C 347 LEU cc_start: 0.8753 (tp) cc_final: 0.8488 (tt) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2380 time to fit residues: 17.9413 Evaluate side-chains 43 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4983 Z= 0.209 Angle : 0.527 5.960 6747 Z= 0.273 Chirality : 0.042 0.144 737 Planarity : 0.004 0.032 873 Dihedral : 5.405 83.820 660 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.10 % Allowed : 7.00 % Favored : 91.90 % 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: 1.22 (0.35), residues: 594 helix: 1.94 (0.34), residues: 245 sheet: 1.05 (0.58), residues: 78 loop : -0.30 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.002 0.001 HIS A 32 PHE 0.010 0.001 PHE C 428 TYR 0.013 0.001 TYR A 145 ARG 0.003 0.000 ARG C 351 *********************** 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 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.610 Fit side-chains REVERT: A 72 ARG cc_start: 0.8330 (mtp-110) cc_final: 0.8053 (mtp-110) REVERT: A 112 ASP cc_start: 0.8713 (m-30) cc_final: 0.8344 (m-30) REVERT: A 140 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7650 (mm-30) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.2216 time to fit residues: 14.5577 Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4983 Z= 0.284 Angle : 0.525 6.569 6747 Z= 0.273 Chirality : 0.042 0.151 737 Planarity : 0.004 0.034 873 Dihedral : 5.512 86.961 660 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.66 % Allowed : 6.81 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.35), residues: 594 helix: 1.73 (0.33), residues: 254 sheet: 1.07 (0.59), residues: 78 loop : -0.42 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 93 HIS 0.002 0.001 HIS C 420 PHE 0.010 0.001 PHE C 522 TYR 0.010 0.001 TYR C 367 ARG 0.006 0.000 ARG C 351 *********************** 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 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.576 Fit side-chains REVERT: A 112 ASP cc_start: 0.8768 (m-30) cc_final: 0.8363 (m-30) REVERT: A 140 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7885 (mm-30) REVERT: C 347 LEU cc_start: 0.8678 (tp) cc_final: 0.8444 (tt) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 0.2263 time to fit residues: 14.2076 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 389 TYR 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: 0.8980 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4983 Z= 0.225 Angle : 0.490 6.089 6747 Z= 0.254 Chirality : 0.041 0.135 737 Planarity : 0.004 0.035 873 Dihedral : 5.246 77.516 660 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.29 % Allowed : 8.47 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.36), residues: 594 helix: 1.76 (0.33), residues: 254 sheet: 1.15 (0.60), residues: 78 loop : -0.39 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR C 367 ARG 0.005 0.000 ARG C 351 *********************** 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 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.542 Fit side-chains REVERT: A 112 ASP cc_start: 0.8728 (m-30) cc_final: 0.8281 (m-30) REVERT: A 140 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7868 (mm-30) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.1935 time to fit residues: 12.1092 Evaluate side-chains 44 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 47 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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: 0.8075 moved from start: 0.1392 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= 0.186 Angle : 0.473 6.853 6747 Z= 0.246 Chirality : 0.041 0.133 737 Planarity : 0.004 0.035 873 Dihedral : 5.008 67.041 660 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.66 % Allowed : 8.47 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.36), residues: 594 helix: 1.80 (0.33), residues: 254 sheet: 1.19 (0.58), residues: 83 loop : -0.38 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR C 367 ARG 0.006 0.000 ARG A 72 *********************** 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 53 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8695 (m-30) cc_final: 0.8238 (m-30) REVERT: A 140 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7785 (mm-30) REVERT: C 347 LEU cc_start: 0.8635 (tp) cc_final: 0.8421 (tt) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.2121 time to fit residues: 13.2734 Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.1420 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= 0.227 Angle : 0.481 6.876 6747 Z= 0.250 Chirality : 0.041 0.134 737 Planarity : 0.004 0.035 873 Dihedral : 4.663 50.379 660 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 8.84 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.36), residues: 594 helix: 1.76 (0.33), residues: 254 sheet: 1.19 (0.58), residues: 83 loop : -0.41 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 407 TYR 0.009 0.001 TYR C 367 ARG 0.006 0.000 ARG A 72 *********************** 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 51 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8716 (m-30) cc_final: 0.8246 (m-30) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.2067 time to fit residues: 12.2484 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 318 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.0050 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.0040 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.3606 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.1432 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= 0.227 Angle : 0.481 6.875 6747 Z= 0.250 Chirality : 0.041 0.134 737 Planarity : 0.004 0.035 873 Dihedral : 4.662 50.379 660 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.10 % Allowed : 9.76 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.36), residues: 594 helix: 1.76 (0.33), residues: 254 sheet: 1.19 (0.58), residues: 83 loop : -0.41 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 407 TYR 0.009 0.001 TYR C 367 ARG 0.006 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8716 (m-30) cc_final: 0.8246 (m-30) outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 0.2254 time to fit residues: 12.8491 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 318 GLN 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: 0.6980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8100 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4983 Z= 0.289 Angle : 0.506 7.561 6747 Z= 0.262 Chirality : 0.042 0.138 737 Planarity : 0.004 0.035 873 Dihedral : 4.367 30.377 660 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.84 % Allowed : 9.02 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.04 (0.36), residues: 594 helix: 1.68 (0.33), residues: 254 sheet: 1.23 (0.59), residues: 83 loop : -0.47 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.001 HIS A 75 PHE 0.011 0.001 PHE C 407 TYR 0.011 0.001 TYR C 367 ARG 0.008 0.000 ARG A 72 *********************** 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 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8748 (m-30) cc_final: 0.8242 (m-30) REVERT: A 140 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7707 (mm-30) REVERT: C 294 MET cc_start: 0.5117 (tpp) cc_final: 0.4754 (tpp) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.2034 time to fit residues: 12.8253 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 318 GLN 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: 0.0970 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4983 Z= 0.228 Angle : 0.485 6.932 6747 Z= 0.252 Chirality : 0.041 0.132 737 Planarity : 0.003 0.035 873 Dihedral : 4.349 30.696 660 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.66 % Allowed : 9.02 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.09 (0.36), residues: 594 helix: 1.75 (0.33), residues: 254 sheet: 1.25 (0.59), residues: 82 loop : -0.49 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 PHE 0.008 0.001 PHE C 407 TYR 0.009 0.001 TYR C 367 ARG 0.003 0.000 ARG C 351 *********************** 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 51 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.586 Fit side-chains REVERT: A 112 ASP cc_start: 0.8625 (m-30) cc_final: 0.8117 (m-30) REVERT: A 140 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 294 MET cc_start: 0.5098 (tpp) cc_final: 0.4746 (tpp) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.2109 time to fit residues: 12.5162 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 425 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 49 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4983 Z= 0.150 Angle : 0.469 6.955 6747 Z= 0.246 Chirality : 0.040 0.133 737 Planarity : 0.003 0.036 873 Dihedral : 4.251 31.458 660 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.10 % Allowed : 9.76 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.36), residues: 594 helix: 1.86 (0.33), residues: 254 sheet: 1.31 (0.59), residues: 82 loop : -0.44 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 93 HIS 0.001 0.000 HIS C 420 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR C 367 ARG 0.004 0.000 ARG A 72 ********************** 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 53 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.624 Fit side-chains REVERT: A 72 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7827 (mtp85) REVERT: A 112 ASP cc_start: 0.8581 (m-30) cc_final: 0.8061 (m-30) REVERT: A 114 ASN cc_start: 0.8830 (t0) cc_final: 0.8464 (t0) REVERT: A 140 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7711 (mm-30) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.2064 time to fit residues: 13.3170 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.0060 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5274 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.126690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.083934 restraints weight = 14777.420| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 5.06 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4983 Z= 0.229 Angle : 0.479 8.550 6747 Z= 0.248 Chirality : 0.041 0.141 737 Planarity : 0.004 0.035 873 Dihedral : 4.252 31.629 660 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.92 % Allowed : 9.94 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.36), residues: 594 helix: 1.84 (0.33), residues: 254 sheet: 1.31 (0.60), residues: 82 loop : -0.48 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 PHE 0.008 0.001 PHE C 407 TYR 0.010 0.001 TYR C 389 ARG 0.003 0.000 ARG C 351 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1377.58 seconds wall clock time: 25 minutes 5.43 seconds (1505.43 seconds total)