Starting phenix.real_space_refine on Mon Mar 11 00:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/03_2024/7li7_23362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/03_2024/7li7_23362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/03_2024/7li7_23362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/03_2024/7li7_23362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/03_2024/7li7_23362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/03_2024/7li7_23362_updated.pdb" } resolution = 4.1 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= 0.001 sd= 0.035 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 34 5.16 5 C 4101 2.51 5 N 960 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 80": "OE1" <-> "OE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6177 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 114 Unusual residues: {'CLR': 1, 'D10': 1, 'D12': 3, 'HP6': 5, 'LNK': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 4.11, per 1000 atoms: 0.67 Number of scatterers: 6177 At special positions: 0 Unit cell: (71.928, 73.224, 121.176, 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 34 16.00 O 1082 8.00 N 960 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 5 sheets defined 46.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 112 Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 122 through 143 Proline residue: A 131 - end of helix removed outlier: 3.841A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 156 through 189 removed outlier: 3.625A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 357 through 390 Processing helix chain 'A' and resid 404 through 416 removed outlier: 4.052A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.836A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 455 through 460 removed outlier: 4.125A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 483 removed outlier: 3.708A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 495 Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 518 through 529 removed outlier: 4.456A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 No H-bonds generated for 'chain 'A' and resid 537 through 540' Processing helix chain 'A' and resid 544 through 558 removed outlier: 3.768A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 587 through 599 Processing helix chain 'A' and resid 604 through 611 Processing sheet with id= A, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.970A pdb=" N ASP B 76 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 87 through 92 Processing sheet with id= C, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.515A pdb=" N ALA C 39 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.328A pdb=" N LYS C 127 " --> pdb=" O LEU C 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.550A pdb=" N PHE C 111 " --> pdb=" O PHE C 60 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 672 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: 1.64 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1814 1.34 - 1.46: 1597 1.46 - 1.58: 2889 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6349 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.64e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.35e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+00 ... (remaining 6344 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 210 107.34 - 114.01: 3529 114.01 - 120.67: 2651 120.67 - 127.34: 2142 127.34 - 134.00: 80 Bond angle restraints: 8612 Sorted by residual: angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 121.70 131.08 -9.38 1.80e+00 3.09e-01 2.71e+01 angle pdb=" N TRP A 197 " pdb=" CA TRP A 197 " pdb=" C TRP A 197 " ideal model delta sigma weight residual 114.56 111.00 3.56 1.27e+00 6.20e-01 7.84e+00 angle pdb=" C13 CLR A 710 " pdb=" C17 CLR A 710 " pdb=" C20 CLR A 710 " ideal model delta sigma weight residual 119.60 112.55 7.05 3.00e+00 1.11e-01 5.52e+00 angle pdb=" C20 CLR A 710 " pdb=" C22 CLR A 710 " pdb=" C23 CLR A 710 " ideal model delta sigma weight residual 115.57 108.76 6.81 3.00e+00 1.11e-01 5.16e+00 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.49 118.10 -2.61 1.24e+00 6.50e-01 4.42e+00 ... (remaining 8607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3379 17.81 - 35.61: 284 35.61 - 53.42: 40 53.42 - 71.23: 5 71.23 - 89.03: 2 Dihedral angle restraints: 3710 sinusoidal: 1510 harmonic: 2200 Sorted by residual: dihedral pdb=" CB GLU A 453 " pdb=" CG GLU A 453 " pdb=" CD GLU A 453 " pdb=" OE1 GLU A 453 " ideal model delta sinusoidal sigma weight residual 0.00 89.03 -89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " pdb=" CD GLU A 136 " pdb=" OE1 GLU A 136 " ideal model delta sinusoidal sigma weight residual 0.00 -84.87 84.87 1 3.00e+01 1.11e-03 9.71e+00 dihedral pdb=" CA ARG A 596 " pdb=" CB ARG A 596 " pdb=" CG ARG A 596 " pdb=" CD ARG A 596 " ideal model delta sinusoidal sigma weight residual 180.00 122.06 57.94 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 945 0.234 - 0.469: 2 0.469 - 0.703: 0 0.703 - 0.937: 0 0.937 - 1.171: 1 Chirality restraints: 948 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-02 2.50e+03 3.43e+03 chirality pdb=" C14 CLR A 710 " pdb=" C13 CLR A 710 " pdb=" C15 CLR A 710 " pdb=" C8 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C9 CLR A 710 " pdb=" C10 CLR A 710 " pdb=" C11 CLR A 710 " pdb=" C8 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 945 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 402 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 403 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 403 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 403 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 100 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO C 101 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.26e-01 pdb=" N PRO A 590 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " -0.014 5.00e-02 4.00e+02 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1876 2.82 - 3.34: 5871 3.34 - 3.86: 10444 3.86 - 4.38: 11371 4.38 - 4.90: 19576 Nonbonded interactions: 49138 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O VAL A 397 " model vdw 2.297 2.440 nonbonded pdb=" O ASN A 112 " pdb=" NZ LYS A 319 " model vdw 2.304 2.520 nonbonded pdb=" O THR A 600 " pdb=" NE ARG A 607 " model vdw 2.304 2.520 nonbonded pdb=" OD1 ASN A 101 " pdb=" NE2 GLN A 332 " model vdw 2.311 2.520 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.313 2.440 ... (remaining 49133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=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: 4.400 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: 13.170 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 21.370 Find NCS groups from input model: 0.180 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: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 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 : 0.002 0.031 6349 Z= 0.148 Angle : 0.611 9.376 8612 Z= 0.297 Chirality : 0.056 1.171 948 Planarity : 0.003 0.034 1047 Dihedral : 12.289 89.034 2305 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.27), residues: 759 helix: -0.80 (0.24), residues: 370 sheet: -1.58 (0.54), residues: 81 loop : -3.08 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 204 HIS 0.001 0.000 HIS A 143 PHE 0.016 0.001 PHE A 474 TYR 0.012 0.001 TYR A 176 ARG 0.006 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4133 (mmmt) cc_final: 0.3539 (mmtp) REVERT: A 260 MET cc_start: 0.6096 (mmm) cc_final: 0.4406 (tmm) REVERT: A 267 TYR cc_start: 0.7045 (t80) cc_final: 0.6839 (t80) REVERT: A 456 HIS cc_start: 0.7952 (p-80) cc_final: 0.7737 (p90) REVERT: A 463 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6779 (mm-30) REVERT: A 478 LEU cc_start: 0.6966 (tt) cc_final: 0.6669 (tp) REVERT: A 514 TRP cc_start: 0.6695 (m100) cc_final: 0.6023 (m-10) REVERT: B 29 GLU cc_start: 0.8859 (mp0) cc_final: 0.8552 (mp0) REVERT: B 88 THR cc_start: 0.9257 (m) cc_final: 0.8963 (p) REVERT: B 125 PHE cc_start: 0.8290 (m-80) cc_final: 0.7888 (m-10) REVERT: C 33 VAL cc_start: 0.8265 (m) cc_final: 0.8057 (p) REVERT: C 66 GLN cc_start: 0.7811 (mp10) cc_final: 0.7283 (mp10) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2146 time to fit residues: 41.7902 Evaluate side-chains 117 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 58 GLN B 132 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6349 Z= 0.227 Angle : 0.560 9.321 8612 Z= 0.295 Chirality : 0.041 0.191 948 Planarity : 0.005 0.058 1047 Dihedral : 5.840 57.847 995 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.31 % Allowed : 5.45 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.29), residues: 759 helix: -0.17 (0.25), residues: 369 sheet: -1.94 (0.49), residues: 92 loop : -2.57 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 PHE 0.020 0.002 PHE A 474 TYR 0.013 0.002 TYR A 410 ARG 0.006 0.001 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4750 (mmmt) cc_final: 0.3920 (mmtt) REVERT: A 267 TYR cc_start: 0.7501 (t80) cc_final: 0.7258 (t80) REVERT: A 514 TRP cc_start: 0.6699 (m100) cc_final: 0.6072 (m-10) REVERT: B 32 LYS cc_start: 0.6273 (mmpt) cc_final: 0.5936 (mmmt) REVERT: B 88 THR cc_start: 0.9463 (m) cc_final: 0.9233 (p) REVERT: C 66 GLN cc_start: 0.8191 (mp10) cc_final: 0.7845 (mp10) REVERT: C 86 PHE cc_start: 0.7604 (m-80) cc_final: 0.7338 (m-80) outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 0.1943 time to fit residues: 35.0325 Evaluate side-chains 115 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6349 Z= 0.230 Angle : 0.545 9.534 8612 Z= 0.281 Chirality : 0.041 0.150 948 Planarity : 0.005 0.065 1047 Dihedral : 5.898 59.710 995 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.82 (0.29), residues: 759 helix: -0.13 (0.26), residues: 365 sheet: -1.73 (0.52), residues: 92 loop : -2.36 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.018 0.001 PHE A 428 TYR 0.016 0.001 TYR A 410 ARG 0.004 0.001 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 197 TRP cc_start: 0.7267 (m-90) cc_final: 0.6392 (m-90) REVERT: A 201 LYS cc_start: 0.4738 (mmmt) cc_final: 0.3823 (mmtt) REVERT: A 267 TYR cc_start: 0.7635 (t80) cc_final: 0.7432 (t80) REVERT: A 456 HIS cc_start: 0.7804 (p90) cc_final: 0.7549 (p90) REVERT: A 478 LEU cc_start: 0.7530 (tt) cc_final: 0.7314 (tp) REVERT: A 514 TRP cc_start: 0.6725 (m100) cc_final: 0.6067 (m-10) REVERT: B 32 LYS cc_start: 0.6205 (mmpt) cc_final: 0.5874 (mmmt) REVERT: B 88 THR cc_start: 0.9508 (m) cc_final: 0.9273 (p) REVERT: C 66 GLN cc_start: 0.8307 (mp10) cc_final: 0.8101 (mp10) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1912 time to fit residues: 34.5607 Evaluate side-chains 114 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 235 HIS ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6349 Z= 0.213 Angle : 0.534 9.566 8612 Z= 0.281 Chirality : 0.040 0.159 948 Planarity : 0.005 0.066 1047 Dihedral : 6.036 59.958 995 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.75 (0.29), residues: 759 helix: -0.11 (0.26), residues: 368 sheet: -1.50 (0.52), residues: 96 loop : -2.35 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.020 0.001 PHE A 474 TYR 0.012 0.001 TYR A 95 ARG 0.004 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8178 (m-10) cc_final: 0.7696 (m-80) REVERT: A 201 LYS cc_start: 0.4958 (mmmt) cc_final: 0.4083 (mmtt) REVERT: A 282 TRP cc_start: 0.6692 (t-100) cc_final: 0.6447 (t-100) REVERT: A 478 LEU cc_start: 0.7603 (tt) cc_final: 0.7366 (tp) REVERT: A 514 TRP cc_start: 0.6644 (m100) cc_final: 0.5981 (m-10) REVERT: A 576 ILE cc_start: 0.7835 (tp) cc_final: 0.7602 (tp) REVERT: B 88 THR cc_start: 0.9512 (m) cc_final: 0.9279 (p) REVERT: C 33 VAL cc_start: 0.8733 (m) cc_final: 0.8527 (p) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1696 time to fit residues: 30.2371 Evaluate side-chains 112 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN A 141 GLN B 58 GLN C 61 GLN C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6349 Z= 0.230 Angle : 0.548 9.536 8612 Z= 0.288 Chirality : 0.040 0.162 948 Planarity : 0.004 0.054 1047 Dihedral : 6.211 59.971 995 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.72 (0.30), residues: 759 helix: -0.14 (0.26), residues: 367 sheet: -1.46 (0.52), residues: 96 loop : -2.27 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.019 0.002 PHE A 474 TYR 0.014 0.001 TYR A 142 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8196 (m-10) cc_final: 0.7654 (m-80) REVERT: A 201 LYS cc_start: 0.5193 (mmmt) cc_final: 0.4143 (mmtt) REVERT: A 414 ILE cc_start: 0.7441 (mm) cc_final: 0.7176 (mm) REVERT: A 514 TRP cc_start: 0.6720 (m100) cc_final: 0.6009 (m-10) REVERT: A 576 ILE cc_start: 0.7904 (tp) cc_final: 0.7633 (tp) REVERT: B 53 MET cc_start: 0.8053 (tpp) cc_final: 0.7707 (mmt) REVERT: B 65 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7003 (mt-10) REVERT: B 88 THR cc_start: 0.9512 (m) cc_final: 0.9273 (p) REVERT: C 33 VAL cc_start: 0.8705 (m) cc_final: 0.8482 (p) REVERT: C 66 GLN cc_start: 0.8358 (mp10) cc_final: 0.7770 (mp10) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1702 time to fit residues: 31.4166 Evaluate side-chains 115 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.0050 chunk 69 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6349 Z= 0.216 Angle : 0.567 9.597 8612 Z= 0.296 Chirality : 0.041 0.212 948 Planarity : 0.005 0.068 1047 Dihedral : 6.277 59.997 995 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.71 (0.30), residues: 759 helix: -0.23 (0.26), residues: 368 sheet: -1.32 (0.53), residues: 96 loop : -2.17 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 PHE 0.021 0.002 PHE A 474 TYR 0.016 0.001 TYR A 142 ARG 0.003 0.000 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8221 (m-10) cc_final: 0.7634 (m-80) REVERT: A 201 LYS cc_start: 0.5179 (mmmt) cc_final: 0.4143 (mmtt) REVERT: A 514 TRP cc_start: 0.6807 (m100) cc_final: 0.6078 (m-10) REVERT: A 576 ILE cc_start: 0.7946 (tp) cc_final: 0.7652 (tp) REVERT: B 65 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7007 (mt-10) REVERT: B 88 THR cc_start: 0.9511 (m) cc_final: 0.9278 (p) REVERT: C 33 VAL cc_start: 0.8717 (m) cc_final: 0.8468 (p) REVERT: C 66 GLN cc_start: 0.8364 (mp10) cc_final: 0.7912 (mp10) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1852 time to fit residues: 33.1382 Evaluate side-chains 119 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 0.0270 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6349 Z= 0.202 Angle : 0.555 9.583 8612 Z= 0.289 Chirality : 0.041 0.200 948 Planarity : 0.004 0.066 1047 Dihedral : 6.280 59.933 995 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.46 (0.31), residues: 759 helix: -0.10 (0.27), residues: 359 sheet: -1.26 (0.53), residues: 96 loop : -1.86 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.018 0.001 PHE A 474 TYR 0.014 0.001 TYR A 107 ARG 0.003 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8194 (m-10) cc_final: 0.7685 (m-80) REVERT: A 201 LYS cc_start: 0.5141 (mmmt) cc_final: 0.4028 (mmmt) REVERT: A 514 TRP cc_start: 0.6855 (m100) cc_final: 0.6150 (m-10) REVERT: A 576 ILE cc_start: 0.7969 (tp) cc_final: 0.7659 (tp) REVERT: A 610 LYS cc_start: 0.7658 (pttp) cc_final: 0.7077 (pttm) REVERT: B 65 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7000 (mt-10) REVERT: B 88 THR cc_start: 0.9508 (m) cc_final: 0.9282 (p) REVERT: C 33 VAL cc_start: 0.8691 (m) cc_final: 0.8481 (p) REVERT: C 66 GLN cc_start: 0.8349 (mp10) cc_final: 0.7792 (mp10) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1610 time to fit residues: 28.9503 Evaluate side-chains 121 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 65 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6349 Z= 0.184 Angle : 0.541 9.563 8612 Z= 0.281 Chirality : 0.040 0.195 948 Planarity : 0.004 0.070 1047 Dihedral : 6.275 59.882 995 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.16 % Allowed : 1.87 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.37 (0.31), residues: 759 helix: -0.04 (0.27), residues: 363 sheet: -1.14 (0.54), residues: 96 loop : -1.83 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.019 0.001 PHE A 474 TYR 0.015 0.001 TYR A 107 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8242 (m-10) cc_final: 0.7753 (m-80) REVERT: A 197 TRP cc_start: 0.7473 (m-90) cc_final: 0.6950 (m-10) REVERT: A 201 LYS cc_start: 0.5200 (mmmt) cc_final: 0.4228 (mmmt) REVERT: A 414 ILE cc_start: 0.7427 (mm) cc_final: 0.7227 (mm) REVERT: A 514 TRP cc_start: 0.6911 (m100) cc_final: 0.6181 (m-10) REVERT: A 536 PHE cc_start: 0.8774 (t80) cc_final: 0.8285 (t80) REVERT: B 65 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6981 (mt-10) REVERT: B 88 THR cc_start: 0.9517 (m) cc_final: 0.9290 (p) REVERT: C 33 VAL cc_start: 0.8721 (m) cc_final: 0.8511 (p) REVERT: C 62 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7661 (tp-100) REVERT: C 66 GLN cc_start: 0.8366 (mp10) cc_final: 0.7701 (mp10) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1674 time to fit residues: 28.0155 Evaluate side-chains 116 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6349 Z= 0.245 Angle : 0.592 9.572 8612 Z= 0.308 Chirality : 0.042 0.181 948 Planarity : 0.005 0.069 1047 Dihedral : 6.471 59.906 995 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.40 (0.30), residues: 759 helix: -0.01 (0.27), residues: 358 sheet: -1.17 (0.54), residues: 96 loop : -1.89 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 PHE 0.020 0.002 PHE A 474 TYR 0.014 0.001 TYR A 107 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8269 (m-10) cc_final: 0.7605 (m-80) REVERT: A 201 LYS cc_start: 0.5575 (mmmt) cc_final: 0.4386 (mmmt) REVERT: A 514 TRP cc_start: 0.6957 (m100) cc_final: 0.6237 (m-10) REVERT: A 536 PHE cc_start: 0.8599 (t80) cc_final: 0.8143 (t80) REVERT: A 576 ILE cc_start: 0.7987 (tp) cc_final: 0.7654 (tp) REVERT: B 65 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 88 THR cc_start: 0.9526 (m) cc_final: 0.9302 (p) REVERT: C 33 VAL cc_start: 0.8781 (m) cc_final: 0.8572 (p) REVERT: C 66 GLN cc_start: 0.8434 (mp10) cc_final: 0.7960 (mp10) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1607 time to fit residues: 26.9695 Evaluate side-chains 112 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 59 optimal weight: 0.0270 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6349 Z= 0.184 Angle : 0.575 10.350 8612 Z= 0.293 Chirality : 0.041 0.190 948 Planarity : 0.005 0.074 1047 Dihedral : 6.418 59.792 995 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.39 (0.30), residues: 759 helix: -0.06 (0.27), residues: 360 sheet: -1.10 (0.55), residues: 96 loop : -1.85 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 537 HIS 0.002 0.001 HIS A 143 PHE 0.019 0.001 PHE A 474 TYR 0.021 0.001 TYR A 176 ARG 0.005 0.000 ARG B 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8208 (m-10) cc_final: 0.7571 (m-80) REVERT: A 201 LYS cc_start: 0.5402 (mmmt) cc_final: 0.4273 (mmmt) REVERT: A 514 TRP cc_start: 0.6965 (m100) cc_final: 0.6229 (m-10) REVERT: A 536 PHE cc_start: 0.9012 (t80) cc_final: 0.8730 (t80) REVERT: B 65 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6966 (mt-10) REVERT: B 88 THR cc_start: 0.9524 (m) cc_final: 0.9301 (p) REVERT: C 33 VAL cc_start: 0.8762 (m) cc_final: 0.8556 (p) REVERT: C 66 GLN cc_start: 0.8428 (mp10) cc_final: 0.7861 (mp10) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1724 time to fit residues: 27.9970 Evaluate side-chains 107 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 368 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.190905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.181753 restraints weight = 7465.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.160729 restraints weight = 10860.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.160253 restraints weight = 13787.948| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6349 Z= 0.200 Angle : 0.583 11.738 8612 Z= 0.298 Chirality : 0.041 0.177 948 Planarity : 0.004 0.071 1047 Dihedral : 6.465 59.650 995 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.36 (0.31), residues: 759 helix: -0.03 (0.27), residues: 360 sheet: -1.09 (0.55), residues: 96 loop : -1.84 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.020 0.001 PHE A 465 TYR 0.017 0.001 TYR A 176 ARG 0.005 0.000 ARG B 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.24 seconds wall clock time: 33 minutes 9.77 seconds (1989.77 seconds total)