Starting phenix.real_space_refine on Tue Feb 13 08:44:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/02_2024/7ey4_31377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/02_2024/7ey4_31377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/02_2024/7ey4_31377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/02_2024/7ey4_31377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/02_2024/7ey4_31377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/02_2024/7ey4_31377.pdb" } resolution = 3.69 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= 0.023 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 17 5.16 5 C 3000 2.51 5 N 772 2.21 5 O 894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "R ARG 346": "NH1" <-> "NH2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 405": "OD1" <-> "OD2" Residue "R GLU 471": "OE1" <-> "OE2" Residue "N PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 224": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4683 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 985 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.25, per 1000 atoms: 0.69 Number of scatterers: 4683 At special positions: 0 Unit cell: (62.13, 80.66, 110.09, 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 17 16.00 O 894 8.00 N 772 7.00 C 3000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.05 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN N 165 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 864.4 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1072 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 11 sheets defined 7.2% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.648A pdb=" N ASP H 31 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.577A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 3.653A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.923A pdb=" N GLU L 70 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.193A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.513A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 47 removed outlier: 4.277A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG H 98 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.668A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 356 through 358 removed outlier: 3.687A pdb=" N ILE R 402 " --> pdb=" O TYR R 508 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'N' and resid 50 through 55 removed outlier: 3.774A pdb=" N ASP N 53 " --> pdb=" O ARG N 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 63 through 64 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 63 through 64 current: chain 'N' and resid 116 through 121 removed outlier: 4.174A pdb=" N ASN N 164 " --> pdb=" O GLU N 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 163 through 164 current: chain 'N' and resid 200 through 205 removed outlier: 5.953A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 252 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: 1.16 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1473 1.35 - 1.48: 1418 1.48 - 1.61: 1891 1.61 - 1.74: 0 1.74 - 1.88: 21 Bond restraints: 4803 Sorted by residual: bond pdb=" CA SER H 107 " pdb=" CB SER H 107 " ideal model delta sigma weight residual 1.532 1.464 0.067 1.82e-02 3.02e+03 1.37e+01 bond pdb=" N CYS N 166 " pdb=" CA CYS N 166 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.58e+00 bond pdb=" N PHE N 168 " pdb=" CA PHE N 168 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.22e-02 6.72e+03 7.54e+00 bond pdb=" CA SER H 104 " pdb=" CB SER H 104 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.22e-02 6.72e+03 7.34e+00 bond pdb=" N ASP H 105 " pdb=" CA ASP H 105 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.04e+00 ... (remaining 4798 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.68: 117 106.68 - 113.53: 2453 113.53 - 120.38: 1840 120.38 - 127.23: 2064 127.23 - 134.08: 45 Bond angle restraints: 6519 Sorted by residual: angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" C VAL L 29 " ideal model delta sigma weight residual 111.90 107.22 4.68 8.10e-01 1.52e+00 3.34e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 127.53 -13.13 2.30e+00 1.89e-01 3.26e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 127.18 -12.78 2.30e+00 1.89e-01 3.09e+01 angle pdb=" N CYS R 379 " pdb=" CA CYS R 379 " pdb=" C CYS R 379 " ideal model delta sigma weight residual 108.38 114.13 -5.75 1.35e+00 5.49e-01 1.82e+01 angle pdb=" N CYS R 432 " pdb=" CA CYS R 432 " pdb=" C CYS R 432 " ideal model delta sigma weight residual 108.60 114.65 -6.05 1.46e+00 4.69e-01 1.71e+01 ... (remaining 6514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 2582 21.25 - 42.51: 184 42.51 - 63.76: 27 63.76 - 85.01: 13 85.01 - 106.26: 12 Dihedral angle restraints: 2818 sinusoidal: 1129 harmonic: 1689 Sorted by residual: dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 180.00 132.41 47.59 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual -86.00 -10.28 -75.72 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CA CYS R 379 " pdb=" C CYS R 379 " pdb=" N TYR R 380 " pdb=" CA TYR R 380 " ideal model delta harmonic sigma weight residual -180.00 -140.32 -39.68 0 5.00e+00 4.00e-02 6.30e+01 ... (remaining 2815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 624 0.078 - 0.156: 70 0.156 - 0.233: 4 0.233 - 0.311: 2 0.311 - 0.389: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.79e+02 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.58e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 698 not shown) Planarity restraints: 836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.322 2.00e-02 2.50e+03 2.72e-01 9.26e+02 pdb=" C7 NAG A 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.471 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.293 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG A 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.007 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO L 8 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.035 5.00e-02 4.00e+02 ... (remaining 833 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 180 2.70 - 3.25: 4472 3.25 - 3.80: 6731 3.80 - 4.35: 8835 4.35 - 4.90: 15297 Nonbonded interactions: 35515 Sorted by model distance: nonbonded pdb=" OH TYR N 37 " pdb=" O LEU N 54 " model vdw 2.150 2.440 nonbonded pdb=" OD1 ASP N 40 " pdb=" OH TYR N 204 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR N 91 " pdb=" OE1 GLU N 191 " model vdw 2.217 2.440 nonbonded pdb=" NH2 ARG H 98 " pdb=" OD2 ASP H 117 " model vdw 2.237 2.520 nonbonded pdb=" NH2 ARG L 31 " pdb=" OE1 GLU R 340 " model vdw 2.241 2.520 ... (remaining 35510 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: 2.950 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: 13.370 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 17.780 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.007 0.068 4803 Z= 0.449 Angle : 0.901 13.127 6519 Z= 0.512 Chirality : 0.053 0.389 701 Planarity : 0.014 0.272 835 Dihedral : 16.811 106.261 1728 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.50 % Favored : 86.15 % Rotamer: Outliers : 0.20 % Allowed : 0.60 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.36 % 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: -2.54 (0.34), residues: 563 helix: -3.57 (0.84), residues: 20 sheet: -0.83 (0.39), residues: 181 loop : -2.14 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 436 HIS 0.001 0.001 HIS N 66 PHE 0.028 0.002 PHE H 56 TYR 0.024 0.002 TYR H 110 ARG 0.017 0.001 ARG N 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.548 Fit side-chains REVERT: H 74 ASP cc_start: 0.8334 (m-30) cc_final: 0.7991 (m-30) REVERT: N 54 LEU cc_start: 0.7149 (mp) cc_final: 0.6142 (mt) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2205 time to fit residues: 33.3479 Evaluate side-chains 98 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN N 164 ASN N 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4803 Z= 0.248 Angle : 0.730 8.443 6519 Z= 0.377 Chirality : 0.049 0.341 701 Planarity : 0.005 0.057 835 Dihedral : 12.511 83.304 708 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.77 % Favored : 90.05 % Rotamer: Outliers : 1.40 % Allowed : 11.60 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.34), residues: 563 helix: -3.55 (0.89), residues: 20 sheet: -0.29 (0.39), residues: 188 loop : -2.07 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 436 HIS 0.000 0.000 HIS N 66 PHE 0.016 0.002 PHE N 43 TYR 0.014 0.001 TYR R 369 ARG 0.007 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 0.554 Fit side-chains REVERT: L 61 ARG cc_start: 0.7805 (ptt90) cc_final: 0.7561 (ptt90) REVERT: H 74 ASP cc_start: 0.8332 (m-30) cc_final: 0.8035 (m-30) REVERT: R 378 LYS cc_start: 0.7697 (ptpt) cc_final: 0.7486 (ptpp) REVERT: R 414 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7208 (mm-40) REVERT: N 64 TRP cc_start: 0.7522 (t60) cc_final: 0.7240 (t60) outliers start: 7 outliers final: 5 residues processed: 114 average time/residue: 0.2104 time to fit residues: 29.1659 Evaluate side-chains 96 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.0050 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 14 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4803 Z= 0.219 Angle : 0.677 7.788 6519 Z= 0.347 Chirality : 0.046 0.229 701 Planarity : 0.005 0.057 835 Dihedral : 10.299 74.755 708 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.24 % Favored : 90.59 % Rotamer: Outliers : 3.00 % Allowed : 14.20 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.97 (0.34), residues: 563 helix: -3.45 (0.88), residues: 20 sheet: -0.12 (0.39), residues: 183 loop : -1.94 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.014 0.001 PHE N 32 TYR 0.014 0.001 TYR R 369 ARG 0.004 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.566 Fit side-chains REVERT: L 61 ARG cc_start: 0.7991 (ptt90) cc_final: 0.7775 (ptt90) REVERT: H 74 ASP cc_start: 0.8378 (m-30) cc_final: 0.8039 (m-30) REVERT: N 64 TRP cc_start: 0.7717 (t60) cc_final: 0.7236 (t60) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.2027 time to fit residues: 26.3881 Evaluate side-chains 97 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 39 GLN R 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4803 Z= 0.352 Angle : 0.722 8.042 6519 Z= 0.374 Chirality : 0.047 0.256 701 Planarity : 0.006 0.090 835 Dihedral : 8.911 60.687 708 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.66 % Favored : 89.17 % Rotamer: Outliers : 6.60 % Allowed : 14.40 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.35), residues: 563 helix: -3.42 (0.85), residues: 20 sheet: -0.30 (0.37), residues: 211 loop : -2.09 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 436 HIS 0.002 0.001 HIS N 49 PHE 0.027 0.002 PHE H 56 TYR 0.019 0.002 TYR H 110 ARG 0.009 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 96 time to evaluate : 0.553 Fit side-chains REVERT: L 81 GLU cc_start: 0.6422 (tp30) cc_final: 0.6041 (tp30) REVERT: H 74 ASP cc_start: 0.8357 (m-30) cc_final: 0.8104 (m-30) outliers start: 33 outliers final: 20 residues processed: 120 average time/residue: 0.2041 time to fit residues: 29.9561 Evaluate side-chains 109 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.0070 chunk 48 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 39 GLN R 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4803 Z= 0.208 Angle : 0.663 8.272 6519 Z= 0.338 Chirality : 0.045 0.237 701 Planarity : 0.005 0.087 835 Dihedral : 7.891 50.887 708 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.60 % Allowed : 16.60 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.86 (0.35), residues: 563 helix: -3.12 (0.93), residues: 20 sheet: 0.04 (0.40), residues: 183 loop : -1.93 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 436 HIS 0.001 0.000 HIS N 49 PHE 0.017 0.001 PHE N 43 TYR 0.012 0.001 TYR H 110 ARG 0.010 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.560 Fit side-chains REVERT: L 38 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8836 (tt0) REVERT: L 81 GLU cc_start: 0.6159 (tp30) cc_final: 0.5863 (tp30) REVERT: N 168 PHE cc_start: 0.8283 (t80) cc_final: 0.8047 (t80) REVERT: N 237 ARG cc_start: 0.8530 (mtm110) cc_final: 0.7826 (mtp-110) outliers start: 23 outliers final: 17 residues processed: 109 average time/residue: 0.2054 time to fit residues: 27.4616 Evaluate side-chains 109 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN R 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 4803 Z= 0.264 Angle : 0.719 17.099 6519 Z= 0.366 Chirality : 0.046 0.215 701 Planarity : 0.005 0.094 835 Dihedral : 7.251 42.202 708 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 6.00 % Allowed : 17.60 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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 (0.35), residues: 563 helix: -2.95 (0.96), residues: 20 sheet: 0.08 (0.38), residues: 202 loop : -2.02 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.019 0.002 PHE N 43 TYR 0.011 0.001 TYR H 110 ARG 0.011 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: L 4 MET cc_start: 0.8274 (mtp) cc_final: 0.8015 (mtp) REVERT: L 81 GLU cc_start: 0.6285 (tp30) cc_final: 0.6027 (tp30) REVERT: N 52 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7627 (tm-30) REVERT: N 237 ARG cc_start: 0.8509 (mtm110) cc_final: 0.8248 (mtp85) outliers start: 30 outliers final: 21 residues processed: 116 average time/residue: 0.1947 time to fit residues: 27.8868 Evaluate side-chains 114 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 39 GLN R 334 ASN N 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4803 Z= 0.232 Angle : 0.708 17.845 6519 Z= 0.361 Chirality : 0.046 0.234 701 Planarity : 0.005 0.094 835 Dihedral : 6.368 39.497 708 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.40 % Allowed : 18.40 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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 (0.35), residues: 563 helix: -2.98 (0.97), residues: 20 sheet: 0.18 (0.40), residues: 183 loop : -1.89 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 436 HIS 0.001 0.000 HIS N 49 PHE 0.026 0.002 PHE N 43 TYR 0.010 0.001 TYR H 110 ARG 0.014 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 0.598 Fit side-chains REVERT: N 52 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7610 (tm-30) REVERT: N 237 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8221 (mtp85) outliers start: 27 outliers final: 20 residues processed: 116 average time/residue: 0.2022 time to fit residues: 28.8053 Evaluate side-chains 115 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 50 optimal weight: 0.4980 chunk 30 optimal weight: 0.0370 chunk 21 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN R 334 ASN R 360 ASN N 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4803 Z= 0.191 Angle : 0.699 16.919 6519 Z= 0.355 Chirality : 0.046 0.235 701 Planarity : 0.005 0.098 835 Dihedral : 5.938 38.576 708 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 4.20 % Allowed : 21.00 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.67 (0.35), residues: 563 helix: -2.79 (1.03), residues: 20 sheet: 0.12 (0.39), residues: 194 loop : -1.83 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 436 HIS 0.001 0.000 HIS N 49 PHE 0.031 0.001 PHE N 43 TYR 0.009 0.001 TYR L 49 ARG 0.014 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.534 Fit side-chains REVERT: N 44 ARG cc_start: 0.5577 (ttm170) cc_final: 0.4599 (mpt180) REVERT: N 52 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7621 (tm-30) REVERT: N 237 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8203 (mtp85) outliers start: 21 outliers final: 17 residues processed: 111 average time/residue: 0.2073 time to fit residues: 28.0429 Evaluate side-chains 110 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain R residue 334 ASN Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN R 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4803 Z= 0.297 Angle : 0.730 16.239 6519 Z= 0.376 Chirality : 0.047 0.257 701 Planarity : 0.006 0.101 835 Dihedral : 5.872 39.209 708 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 5.60 % Allowed : 20.40 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.35), residues: 563 helix: -2.82 (1.00), residues: 20 sheet: 0.14 (0.39), residues: 193 loop : -1.98 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 97 HIS 0.001 0.001 HIS N 49 PHE 0.030 0.002 PHE N 43 TYR 0.014 0.001 TYR H 110 ARG 0.015 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.547 Fit side-chains REVERT: N 44 ARG cc_start: 0.5749 (ttm170) cc_final: 0.4537 (mpt180) REVERT: N 52 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7697 (tm-30) REVERT: N 237 ARG cc_start: 0.8484 (mtm110) cc_final: 0.8198 (mtp85) outliers start: 28 outliers final: 23 residues processed: 115 average time/residue: 0.1991 time to fit residues: 28.1235 Evaluate side-chains 119 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN R 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4803 Z= 0.286 Angle : 0.732 15.688 6519 Z= 0.379 Chirality : 0.047 0.241 701 Planarity : 0.006 0.095 835 Dihedral : 5.768 38.662 708 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.20 % Allowed : 20.80 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.74 (0.35), residues: 563 helix: -3.24 (0.80), residues: 26 sheet: 0.09 (0.38), residues: 193 loop : -1.82 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 97 HIS 0.002 0.001 HIS N 49 PHE 0.029 0.002 PHE N 43 TYR 0.013 0.001 TYR H 110 ARG 0.014 0.001 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.509 Fit side-chains REVERT: R 493 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7958 (mm-40) REVERT: N 44 ARG cc_start: 0.5956 (ttm170) cc_final: 0.4441 (mpt180) REVERT: N 52 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7740 (tm-30) REVERT: N 237 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8177 (mtp85) outliers start: 26 outliers final: 24 residues processed: 111 average time/residue: 0.2123 time to fit residues: 28.7996 Evaluate side-chains 118 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.0050 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112939 restraints weight = 6538.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115017 restraints weight = 4988.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116337 restraints weight = 4201.558| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4803 Z= 0.216 Angle : 0.697 14.610 6519 Z= 0.360 Chirality : 0.045 0.228 701 Planarity : 0.005 0.093 835 Dihedral : 5.472 37.419 708 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 5.00 % Allowed : 21.20 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.69 (0.35), residues: 563 helix: -3.20 (0.81), residues: 26 sheet: 0.13 (0.38), residues: 196 loop : -1.81 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 97 HIS 0.001 0.001 HIS N 49 PHE 0.029 0.001 PHE N 43 TYR 0.011 0.001 TYR L 49 ARG 0.014 0.001 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.56 seconds wall clock time: 28 minutes 18.16 seconds (1698.16 seconds total)