Starting phenix.real_space_refine on Fri Mar 15 03:19:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9e_24934/03_2024/7s9e_24934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9e_24934/03_2024/7s9e_24934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9e_24934/03_2024/7s9e_24934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9e_24934/03_2024/7s9e_24934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9e_24934/03_2024/7s9e_24934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9e_24934/03_2024/7s9e_24934_updated.pdb" } resolution = 3.7 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= 0.005 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 48 5.16 5 C 6870 2.51 5 N 1682 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B GLU 721": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5228 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5228 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SAL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SAL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.87, per 1000 atoms: 0.56 Number of scatterers: 10476 At special positions: 0 Unit cell: (117.993, 113.741, 113.741, 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 48 16.00 O 1876 8.00 N 1682 7.00 C 6870 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=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 4 sheets defined 58.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 79 through 105 Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 126 removed outlier: 4.465A pdb=" N TYR A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 169 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 207 through 229 Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 259 through 279 Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 340 through 364 removed outlier: 3.838A pdb=" N LYS A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 397 through 406 Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 437 through 464 removed outlier: 4.670A pdb=" N GLY A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE A 455 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Proline residue: A 459 - end of helix Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'A' and resid 485 through 503 removed outlier: 3.708A pdb=" N THR A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 564 through 578 Processing helix chain 'A' and resid 654 through 670 Processing helix chain 'A' and resid 681 through 689 Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 79 through 105 Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 126 removed outlier: 4.465A pdb=" N TYR B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 169 through 195 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 207 through 229 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 259 through 279 Processing helix chain 'B' and resid 292 through 307 Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 340 through 364 removed outlier: 3.837A pdb=" N LYS B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 437 through 464 removed outlier: 4.670A pdb=" N GLY B 450 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N MET B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Proline residue: B 459 - end of helix Processing helix chain 'B' and resid 466 through 480 Processing helix chain 'B' and resid 485 through 503 removed outlier: 3.708A pdb=" N THR B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 564 through 578 Processing helix chain 'B' and resid 654 through 670 Processing helix chain 'B' and resid 681 through 689 Processing helix chain 'B' and resid 698 through 700 No H-bonds generated for 'chain 'B' and resid 698 through 700' Processing helix chain 'B' and resid 706 through 720 Processing sheet with id= A, first strand: chain 'A' and resid 511 through 513 Processing sheet with id= B, first strand: chain 'A' and resid 535 through 539 removed outlier: 6.577A pdb=" N THR A 641 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE A 538 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 643 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR A 673 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU A 644 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 675 " --> pdb=" O LEU A 644 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 511 through 513 Processing sheet with id= D, first strand: chain 'B' and resid 535 through 539 removed outlier: 6.578A pdb=" N THR B 641 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE B 538 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE B 643 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR B 673 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU B 644 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR B 675 " --> pdb=" O LEU B 644 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 544 hydrogen bonds defined for protein. 1536 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: 2.64 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3176 1.34 - 1.46: 2107 1.46 - 1.58: 5351 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 10712 Sorted by residual: bond pdb=" N VAL B 27 " pdb=" CA VAL B 27 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.20e-02 6.94e+03 9.18e+00 bond pdb=" N ILE B 22 " pdb=" CA ILE B 22 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.29e-02 6.01e+03 8.87e+00 bond pdb=" N ILE A 494 " pdb=" CA ILE A 494 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.70e+00 bond pdb=" N ILE A 22 " pdb=" CA ILE A 22 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.29e-02 6.01e+03 8.54e+00 bond pdb=" N ILE B 494 " pdb=" CA ILE B 494 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.38e+00 ... (remaining 10707 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.80: 210 104.80 - 112.10: 5357 112.10 - 119.41: 3399 119.41 - 126.71: 5486 126.71 - 134.02: 108 Bond angle restraints: 14560 Sorted by residual: angle pdb=" C GLU B 694 " pdb=" N ASN B 695 " pdb=" CA ASN B 695 " ideal model delta sigma weight residual 122.83 127.56 -4.73 1.08e+00 8.57e-01 1.92e+01 angle pdb=" C GLU A 694 " pdb=" N ASN A 695 " pdb=" CA ASN A 695 " ideal model delta sigma weight residual 122.83 127.56 -4.73 1.08e+00 8.57e-01 1.91e+01 angle pdb=" CA SER B 24 " pdb=" C SER B 24 " pdb=" O SER B 24 " ideal model delta sigma weight residual 121.87 117.24 4.63 1.16e+00 7.43e-01 1.59e+01 angle pdb=" N SER A 24 " pdb=" CA SER A 24 " pdb=" C SER A 24 " ideal model delta sigma weight residual 110.53 105.46 5.07 1.29e+00 6.01e-01 1.54e+01 angle pdb=" CA SER A 24 " pdb=" C SER A 24 " pdb=" O SER A 24 " ideal model delta sigma weight residual 121.94 117.49 4.45 1.15e+00 7.56e-01 1.50e+01 ... (remaining 14555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5760 17.92 - 35.85: 482 35.85 - 53.77: 80 53.77 - 71.69: 4 71.69 - 89.62: 8 Dihedral angle restraints: 6334 sinusoidal: 2428 harmonic: 3906 Sorted by residual: dihedral pdb=" CA ASN B 695 " pdb=" C ASN B 695 " pdb=" N PRO B 696 " pdb=" CA PRO B 696 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ASN A 695 " pdb=" C ASN A 695 " pdb=" N PRO A 696 " pdb=" CA PRO A 696 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA VAL B 268 " pdb=" C VAL B 268 " pdb=" N PHE B 269 " pdb=" CA PHE B 269 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 6331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1145 0.040 - 0.080: 392 0.080 - 0.120: 167 0.120 - 0.160: 17 0.160 - 0.200: 5 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CB THR B 128 " pdb=" CA THR B 128 " pdb=" OG1 THR B 128 " pdb=" CG2 THR B 128 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CB THR A 128 " pdb=" CA THR A 128 " pdb=" OG1 THR A 128 " pdb=" CG2 THR A 128 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1723 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 288 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 289 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 288 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO B 289 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 21 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C PRO A 21 " -0.030 2.00e-02 2.50e+03 pdb=" O PRO A 21 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 22 " 0.010 2.00e-02 2.50e+03 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 994 2.74 - 3.28: 11517 3.28 - 3.82: 17446 3.82 - 4.36: 20156 4.36 - 4.90: 34066 Nonbonded interactions: 84179 Sorted by model distance: nonbonded pdb=" OG SER B 167 " pdb=" OE1 GLU B 169 " model vdw 2.202 2.440 nonbonded pdb=" OG SER A 167 " pdb=" OE1 GLU A 169 " model vdw 2.202 2.440 nonbonded pdb=" OG SER B 41 " pdb=" O ASP B 44 " model vdw 2.214 2.440 nonbonded pdb=" OG SER A 41 " pdb=" O ASP A 44 " model vdw 2.215 2.440 nonbonded pdb=" O PHE B 101 " pdb=" OG SER B 141 " model vdw 2.225 2.440 ... (remaining 84174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 4.170 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.940 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 0.038 10712 Z= 0.242 Angle : 0.721 9.226 14560 Z= 0.411 Chirality : 0.047 0.200 1726 Planarity : 0.004 0.045 1816 Dihedral : 13.528 89.618 3834 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.23), residues: 1346 helix: 0.73 (0.18), residues: 838 sheet: 1.28 (0.94), residues: 36 loop : -2.17 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.004 0.001 HIS B 25 PHE 0.021 0.002 PHE B 198 TYR 0.012 0.001 TYR A 16 ARG 0.007 0.001 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8118 (m-10) cc_final: 0.7696 (m-10) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2003 time to fit residues: 43.5501 Evaluate side-chains 111 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 0.0170 chunk 54 optimal weight: 0.0670 chunk 105 optimal weight: 0.3980 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 121 optimal weight: 0.0870 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10712 Z= 0.164 Angle : 0.573 5.920 14560 Z= 0.287 Chirality : 0.044 0.173 1726 Planarity : 0.004 0.046 1816 Dihedral : 4.926 47.668 1450 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.96 % Allowed : 7.58 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.24), residues: 1346 helix: 1.05 (0.18), residues: 840 sheet: 1.40 (0.92), residues: 36 loop : -1.84 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 472 HIS 0.003 0.001 HIS A 33 PHE 0.013 0.001 PHE B 198 TYR 0.017 0.001 TYR A 228 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: B 326 LEU cc_start: 0.8421 (mt) cc_final: 0.7976 (mt) outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.2010 time to fit residues: 41.0122 Evaluate side-chains 120 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 121 optimal weight: 0.1980 chunk 131 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 120 optimal weight: 0.0980 chunk 41 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10712 Z= 0.166 Angle : 0.538 9.251 14560 Z= 0.267 Chirality : 0.042 0.143 1726 Planarity : 0.004 0.047 1816 Dihedral : 4.619 41.716 1450 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.66 % Allowed : 10.10 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.24), residues: 1346 helix: 1.31 (0.18), residues: 844 sheet: 1.62 (0.94), residues: 36 loop : -1.76 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 472 HIS 0.002 0.001 HIS A 131 PHE 0.012 0.001 PHE A 278 TYR 0.018 0.001 TYR B 578 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.8563 (mmm) cc_final: 0.7666 (mmm) REVERT: A 326 LEU cc_start: 0.8228 (mt) cc_final: 0.7813 (mt) REVERT: B 225 MET cc_start: 0.8547 (mmm) cc_final: 0.7715 (mmm) REVERT: B 326 LEU cc_start: 0.8368 (mt) cc_final: 0.7903 (mt) outliers start: 19 outliers final: 14 residues processed: 132 average time/residue: 0.1865 time to fit residues: 37.8935 Evaluate side-chains 126 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 527 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 0.0970 chunk 122 optimal weight: 0.0670 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10712 Z= 0.154 Angle : 0.518 5.650 14560 Z= 0.258 Chirality : 0.042 0.146 1726 Planarity : 0.004 0.047 1816 Dihedral : 4.446 37.378 1450 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.74 % Allowed : 12.37 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.24), residues: 1346 helix: 1.49 (0.19), residues: 842 sheet: 1.67 (0.94), residues: 36 loop : -1.76 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.002 0.001 HIS A 337 PHE 0.011 0.001 PHE B 278 TYR 0.011 0.001 TYR A 545 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.8668 (mmm) cc_final: 0.7561 (mmm) REVERT: A 326 LEU cc_start: 0.8145 (mt) cc_final: 0.7755 (mt) REVERT: B 225 MET cc_start: 0.8655 (mmm) cc_final: 0.7566 (mmm) REVERT: B 326 LEU cc_start: 0.8269 (mt) cc_final: 0.7827 (mt) outliers start: 20 outliers final: 16 residues processed: 134 average time/residue: 0.1735 time to fit residues: 35.6834 Evaluate side-chains 125 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 527 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 overall best weight: 1.0094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10712 Z= 0.192 Angle : 0.532 6.566 14560 Z= 0.266 Chirality : 0.042 0.153 1726 Planarity : 0.004 0.047 1816 Dihedral : 4.365 34.788 1450 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.44 % Allowed : 13.41 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1346 helix: 1.47 (0.19), residues: 846 sheet: 1.78 (0.96), residues: 36 loop : -1.78 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 472 HIS 0.002 0.001 HIS A 704 PHE 0.012 0.001 PHE A 278 TYR 0.019 0.001 TYR A 578 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8214 (mt) cc_final: 0.7817 (mt) REVERT: A 577 LYS cc_start: 0.7550 (tmtt) cc_final: 0.7152 (tmtt) REVERT: B 326 LEU cc_start: 0.8286 (mt) cc_final: 0.7830 (mt) REVERT: B 577 LYS cc_start: 0.7543 (tmtt) cc_final: 0.7172 (tmtt) outliers start: 28 outliers final: 22 residues processed: 133 average time/residue: 0.1802 time to fit residues: 36.6606 Evaluate side-chains 128 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.0020 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 31 optimal weight: 0.0770 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10712 Z= 0.154 Angle : 0.530 10.399 14560 Z= 0.258 Chirality : 0.042 0.155 1726 Planarity : 0.004 0.048 1816 Dihedral : 4.270 32.046 1450 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.53 % Allowed : 13.59 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1346 helix: 1.59 (0.19), residues: 846 sheet: 1.82 (0.94), residues: 36 loop : -1.76 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 70 HIS 0.002 0.001 HIS A 131 PHE 0.010 0.001 PHE B 278 TYR 0.016 0.001 TYR B 578 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.8647 (mmm) cc_final: 0.7675 (mmm) REVERT: A 326 LEU cc_start: 0.8149 (mt) cc_final: 0.7867 (mt) REVERT: A 577 LYS cc_start: 0.7575 (tmtt) cc_final: 0.7227 (tmtt) REVERT: B 225 MET cc_start: 0.8652 (mmm) cc_final: 0.7392 (mmm) REVERT: B 326 LEU cc_start: 0.8238 (mt) cc_final: 0.7882 (mt) REVERT: B 645 ASP cc_start: 0.8135 (t70) cc_final: 0.7775 (t0) REVERT: B 665 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7722 (ttpt) outliers start: 29 outliers final: 21 residues processed: 136 average time/residue: 0.1855 time to fit residues: 38.2237 Evaluate side-chains 131 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.0040 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10712 Z= 0.224 Angle : 0.560 9.339 14560 Z= 0.276 Chirality : 0.043 0.152 1726 Planarity : 0.004 0.047 1816 Dihedral : 4.299 30.744 1450 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.40 % Allowed : 12.98 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.24), residues: 1346 helix: 1.53 (0.19), residues: 850 sheet: 1.82 (0.90), residues: 36 loop : -1.78 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.004 0.001 HIS B 707 PHE 0.012 0.001 PHE B 278 TYR 0.012 0.001 TYR B 546 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.8553 (mmm) cc_final: 0.7517 (mmm) REVERT: A 326 LEU cc_start: 0.8184 (mt) cc_final: 0.7891 (mt) REVERT: A 577 LYS cc_start: 0.7523 (tmtt) cc_final: 0.7243 (tmtt) REVERT: B 225 MET cc_start: 0.8547 (mmm) cc_final: 0.7541 (mmm) REVERT: B 326 LEU cc_start: 0.8257 (mt) cc_final: 0.7878 (mt) REVERT: B 645 ASP cc_start: 0.8212 (t70) cc_final: 0.7911 (t0) outliers start: 39 outliers final: 35 residues processed: 139 average time/residue: 0.1875 time to fit residues: 40.4438 Evaluate side-chains 139 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 454 GLN B 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10712 Z= 0.207 Angle : 0.549 9.222 14560 Z= 0.271 Chirality : 0.043 0.158 1726 Planarity : 0.004 0.047 1816 Dihedral : 4.308 29.244 1450 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.31 % Allowed : 13.85 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1346 helix: 1.55 (0.19), residues: 850 sheet: 2.02 (0.89), residues: 36 loop : -1.74 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 70 HIS 0.002 0.001 HIS B 707 PHE 0.012 0.001 PHE A 278 TYR 0.010 0.001 TYR A 16 ARG 0.003 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.8561 (mmm) cc_final: 0.7616 (mmm) REVERT: A 326 LEU cc_start: 0.8188 (mt) cc_final: 0.7809 (mt) REVERT: A 577 LYS cc_start: 0.7605 (tmtt) cc_final: 0.7329 (tmtt) REVERT: B 225 MET cc_start: 0.8523 (mmm) cc_final: 0.7577 (mmm) REVERT: B 326 LEU cc_start: 0.8326 (mt) cc_final: 0.7920 (mt) REVERT: B 645 ASP cc_start: 0.8199 (t70) cc_final: 0.7841 (t0) outliers start: 38 outliers final: 34 residues processed: 133 average time/residue: 0.1717 time to fit residues: 34.9453 Evaluate side-chains 139 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 113 optimal weight: 0.2980 chunk 119 optimal weight: 0.0770 chunk 79 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10712 Z= 0.174 Angle : 0.537 8.767 14560 Z= 0.263 Chirality : 0.042 0.160 1726 Planarity : 0.004 0.047 1816 Dihedral : 4.219 27.113 1450 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.79 % Allowed : 14.81 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.25), residues: 1346 helix: 1.64 (0.19), residues: 848 sheet: 2.19 (0.88), residues: 36 loop : -1.62 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 70 HIS 0.002 0.001 HIS B 707 PHE 0.011 0.001 PHE B 241 TYR 0.022 0.001 TYR A 578 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.8615 (mmm) cc_final: 0.7574 (mmm) REVERT: A 316 ASP cc_start: 0.8361 (t0) cc_final: 0.7918 (t0) REVERT: A 326 LEU cc_start: 0.8186 (mt) cc_final: 0.7849 (mt) REVERT: A 577 LYS cc_start: 0.7626 (tmtt) cc_final: 0.7221 (tmtt) REVERT: B 225 MET cc_start: 0.8629 (mmm) cc_final: 0.7625 (mmm) REVERT: B 326 LEU cc_start: 0.8330 (mt) cc_final: 0.7954 (mt) REVERT: B 645 ASP cc_start: 0.8196 (t70) cc_final: 0.7780 (t0) outliers start: 32 outliers final: 31 residues processed: 127 average time/residue: 0.1870 time to fit residues: 36.2726 Evaluate side-chains 131 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 122 optimal weight: 0.0040 chunk 106 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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: 0.7880 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10712 Z= 0.164 Angle : 0.539 8.628 14560 Z= 0.263 Chirality : 0.042 0.171 1726 Planarity : 0.004 0.048 1816 Dihedral : 4.179 25.566 1450 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.26 % Allowed : 15.51 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.25), residues: 1346 helix: 1.66 (0.19), residues: 850 sheet: 2.35 (0.88), residues: 36 loop : -1.59 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 472 HIS 0.002 0.001 HIS B 131 PHE 0.011 0.001 PHE B 241 TYR 0.020 0.001 TYR A 578 ARG 0.003 0.000 ARG B 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.8598 (mmm) cc_final: 0.7556 (mmm) REVERT: A 316 ASP cc_start: 0.8352 (t0) cc_final: 0.7905 (t0) REVERT: A 326 LEU cc_start: 0.8115 (mt) cc_final: 0.7723 (mt) REVERT: A 497 MET cc_start: 0.7852 (mmp) cc_final: 0.7603 (mmp) REVERT: A 577 LYS cc_start: 0.7628 (tmtt) cc_final: 0.7342 (tmtt) REVERT: B 225 MET cc_start: 0.8621 (mmm) cc_final: 0.7605 (mmm) REVERT: B 326 LEU cc_start: 0.8318 (mt) cc_final: 0.7942 (mt) REVERT: B 645 ASP cc_start: 0.8199 (t70) cc_final: 0.7770 (t0) outliers start: 26 outliers final: 26 residues processed: 121 average time/residue: 0.1843 time to fit residues: 33.9764 Evaluate side-chains 127 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 109 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 707 HIS B 548 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098425 restraints weight = 17097.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098541 restraints weight = 17441.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100045 restraints weight = 11780.316| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10712 Z= 0.165 Angle : 0.534 8.458 14560 Z= 0.263 Chirality : 0.042 0.165 1726 Planarity : 0.004 0.048 1816 Dihedral : 4.120 24.427 1450 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.87 % Allowed : 15.07 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.25), residues: 1346 helix: 1.73 (0.19), residues: 844 sheet: 2.50 (0.88), residues: 36 loop : -1.48 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.002 0.001 HIS A 337 PHE 0.011 0.001 PHE B 241 TYR 0.022 0.001 TYR A 578 ARG 0.003 0.000 ARG B 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.21 seconds wall clock time: 35 minutes 55.83 seconds (2155.83 seconds total)