Starting phenix.real_space_refine on Tue Feb 13 06:29:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/02_2024/7n98_24252.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/02_2024/7n98_24252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/02_2024/7n98_24252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/02_2024/7n98_24252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/02_2024/7n98_24252.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/02_2024/7n98_24252.pdb" } resolution = 3.5 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= 1.000 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 20 5.16 5 C 2412 2.51 5 N 572 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 504": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3625 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3625 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 22, 'TRANS': 450} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 2.54, per 1000 atoms: 0.70 Number of scatterers: 3625 At special positions: 0 Unit cell: (79.12, 71.38, 85.14, 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 20 16.00 O 621 8.00 N 572 7.00 C 2412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 464 " 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=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 817.2 milliseconds 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 1 sheets defined 74.6% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.917A pdb=" N GLY A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 4.275A pdb=" N GLN A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 64 " --> pdb=" O CYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 77 through 105 removed outlier: 3.712A pdb=" N ASP A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.724A pdb=" N SER A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.521A pdb=" N ILE A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 4.653A pdb=" N ILE A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.810A pdb=" N LEU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 179 through 209 removed outlier: 4.145A pdb=" N ASP A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 266 removed outlier: 3.740A pdb=" N LEU A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.688A pdb=" N MET A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 323 removed outlier: 3.505A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.883A pdb=" N LEU A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.768A pdb=" N LEU A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 379 Proline residue: A 373 - end of helix removed outlier: 3.813A pdb=" N ALA A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 removed outlier: 3.535A pdb=" N VAL A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 409 through 420 removed outlier: 3.699A pdb=" N VAL A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 4.058A pdb=" N PHE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 493 removed outlier: 3.956A pdb=" N LYS A 475 " --> pdb=" O LYS A 471 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 498 through 509 removed outlier: 4.732A pdb=" N LYS A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 218 214 hydrogen bonds defined for protein. 642 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: 0.86 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1088 1.34 - 1.46: 750 1.46 - 1.58: 1857 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3725 Sorted by residual: bond pdb=" N LYS A 440 " pdb=" CA LYS A 440 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.25e+00 bond pdb=" N ALA A 53 " pdb=" CA ALA A 53 " ideal model delta sigma weight residual 1.463 1.456 0.007 6.90e-03 2.10e+04 1.16e+00 bond pdb=" C GLY A 52 " pdb=" N ALA A 53 " ideal model delta sigma weight residual 1.341 1.323 0.017 1.65e-02 3.67e+03 1.09e+00 bond pdb=" C VAL A 135 " pdb=" N PRO A 136 " ideal model delta sigma weight residual 1.332 1.324 0.008 8.20e-03 1.49e+04 1.01e+00 bond pdb=" N PRO A 136 " pdb=" CA PRO A 136 " ideal model delta sigma weight residual 1.473 1.465 0.008 8.50e-03 1.38e+04 8.95e-01 ... (remaining 3720 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.80: 112 106.80 - 113.63: 2035 113.63 - 120.46: 1577 120.46 - 127.29: 1317 127.29 - 134.11: 42 Bond angle restraints: 5083 Sorted by residual: angle pdb=" N VAL A 372 " pdb=" CA VAL A 372 " pdb=" C VAL A 372 " ideal model delta sigma weight residual 108.88 115.75 -6.87 2.16e+00 2.14e-01 1.01e+01 angle pdb=" C MET A 409 " pdb=" N LEU A 410 " pdb=" CA LEU A 410 " ideal model delta sigma weight residual 120.09 123.82 -3.73 1.25e+00 6.40e-01 8.89e+00 angle pdb=" C GLY A 52 " pdb=" N ALA A 53 " pdb=" CA ALA A 53 " ideal model delta sigma weight residual 119.83 122.80 -2.97 1.11e+00 8.12e-01 7.16e+00 angle pdb=" N LYS A 440 " pdb=" CA LYS A 440 " pdb=" C LYS A 440 " ideal model delta sigma weight residual 111.28 108.53 2.75 1.09e+00 8.42e-01 6.39e+00 angle pdb=" C ALA A 53 " pdb=" CA ALA A 53 " pdb=" CB ALA A 53 " ideal model delta sigma weight residual 113.57 109.70 3.87 1.57e+00 4.06e-01 6.09e+00 ... (remaining 5078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 1934 15.76 - 31.52: 165 31.52 - 47.28: 43 47.28 - 63.04: 11 63.04 - 78.81: 4 Dihedral angle restraints: 2157 sinusoidal: 780 harmonic: 1377 Sorted by residual: dihedral pdb=" CA GLU A 382 " pdb=" C GLU A 382 " pdb=" N ARG A 383 " pdb=" CA ARG A 383 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA VAL A 372 " pdb=" C VAL A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ALA A 53 " pdb=" C ALA A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta harmonic sigma weight residual 180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 2154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 407 0.041 - 0.082: 143 0.082 - 0.123: 41 0.123 - 0.164: 5 0.164 - 0.205: 2 Chirality restraints: 598 Sorted by residual: chirality pdb=" CB ILE A 486 " pdb=" CA ILE A 486 " pdb=" CG1 ILE A 486 " pdb=" CG2 ILE A 486 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO A 54 " pdb=" N PRO A 54 " pdb=" C PRO A 54 " pdb=" CB PRO A 54 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA PRO A 425 " pdb=" N PRO A 425 " pdb=" C PRO A 425 " pdb=" CB PRO A 425 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 595 not shown) Planarity restraints: 627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 466 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO A 467 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 53 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 54 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 496 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 497 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " 0.027 5.00e-02 4.00e+02 ... (remaining 624 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 584 2.75 - 3.29: 3814 3.29 - 3.83: 5785 3.83 - 4.36: 6120 4.36 - 4.90: 10383 Nonbonded interactions: 26686 Sorted by model distance: nonbonded pdb=" CE MET A 409 " pdb=" CD2 LEU A 495 " model vdw 2.217 3.880 nonbonded pdb=" O PHE A 358 " pdb=" OG1 THR A 362 " model vdw 2.228 2.440 nonbonded pdb=" OD1 ASN A 318 " pdb=" OG SER A 450 " model vdw 2.300 2.440 nonbonded pdb=" O ILE A 176 " pdb=" OG SER A 177 " model vdw 2.336 2.440 nonbonded pdb=" OE2 GLU A 500 " pdb=" NH2 ARG A 503 " model vdw 2.337 2.520 ... (remaining 26681 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: 0.610 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: 2.770 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.670 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3725 Z= 0.267 Angle : 0.720 6.867 5083 Z= 0.403 Chirality : 0.046 0.205 598 Planarity : 0.006 0.064 627 Dihedral : 13.694 78.806 1266 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.27 % Allowed : 0.54 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.40), residues: 471 helix: -0.05 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -3.04 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 407 HIS 0.002 0.001 HIS A 423 PHE 0.016 0.002 PHE A 285 TYR 0.013 0.002 TYR A 435 ARG 0.005 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.404 Fit side-chains REVERT: A 300 LYS cc_start: 0.8549 (mttt) cc_final: 0.7984 (tttm) REVERT: A 361 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8340 (tptp) REVERT: A 503 ARG cc_start: 0.8368 (mtm180) cc_final: 0.7986 (ptm160) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1161 time to fit residues: 15.2056 Evaluate side-chains 81 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3725 Z= 0.201 Angle : 0.626 6.753 5083 Z= 0.322 Chirality : 0.044 0.165 598 Planarity : 0.005 0.054 627 Dihedral : 4.944 24.082 501 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.80 % Allowed : 14.21 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.41), residues: 471 helix: 0.39 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -3.04 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.001 0.000 HIS A 146 PHE 0.025 0.002 PHE A 134 TYR 0.012 0.001 TYR A 129 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 68 ILE cc_start: 0.8179 (tp) cc_final: 0.7946 (tp) REVERT: A 72 ASP cc_start: 0.8517 (m-30) cc_final: 0.8212 (m-30) REVERT: A 137 ASP cc_start: 0.7438 (t0) cc_final: 0.7063 (t0) REVERT: A 300 LYS cc_start: 0.8540 (mttt) cc_final: 0.7901 (tttm) REVERT: A 361 LYS cc_start: 0.8582 (tmtt) cc_final: 0.8049 (tptp) REVERT: A 381 MET cc_start: 0.5171 (ttt) cc_final: 0.4736 (ttm) REVERT: A 409 MET cc_start: 0.7750 (ttt) cc_final: 0.7465 (mtp) REVERT: A 503 ARG cc_start: 0.8315 (mtm180) cc_final: 0.7510 (ptm160) outliers start: 3 outliers final: 3 residues processed: 94 average time/residue: 0.1213 time to fit residues: 14.8660 Evaluate side-chains 88 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.0050 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 overall best weight: 0.9334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3725 Z= 0.205 Angle : 0.609 6.652 5083 Z= 0.311 Chirality : 0.044 0.174 598 Planarity : 0.005 0.051 627 Dihedral : 4.731 22.947 501 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.14 % Allowed : 19.03 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.41), residues: 471 helix: 0.56 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -3.01 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.002 0.000 HIS A 146 PHE 0.032 0.001 PHE A 134 TYR 0.011 0.001 TYR A 55 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 68 ILE cc_start: 0.8127 (tp) cc_final: 0.7910 (tp) REVERT: A 72 ASP cc_start: 0.8495 (m-30) cc_final: 0.8174 (m-30) REVERT: A 137 ASP cc_start: 0.7431 (t0) cc_final: 0.6951 (t0) REVERT: A 300 LYS cc_start: 0.8580 (mttt) cc_final: 0.7961 (tttm) REVERT: A 361 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8051 (tptp) REVERT: A 381 MET cc_start: 0.5107 (ttt) cc_final: 0.4678 (ttm) REVERT: A 409 MET cc_start: 0.7892 (ttt) cc_final: 0.7665 (mtp) REVERT: A 466 GLN cc_start: 0.6848 (pt0) cc_final: 0.6444 (pt0) REVERT: A 503 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7778 (ptm160) outliers start: 8 outliers final: 7 residues processed: 94 average time/residue: 0.1137 time to fit residues: 14.0010 Evaluate side-chains 90 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3725 Z= 0.188 Angle : 0.576 6.540 5083 Z= 0.295 Chirality : 0.043 0.165 598 Planarity : 0.005 0.054 627 Dihedral : 4.569 22.597 501 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.02 % Allowed : 20.11 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.41), residues: 471 helix: 0.73 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.91 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 91 HIS 0.001 0.000 HIS A 146 PHE 0.032 0.001 PHE A 134 TYR 0.015 0.001 TYR A 55 ARG 0.004 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7289 (t0) cc_final: 0.6767 (t0) REVERT: A 164 CYS cc_start: 0.9341 (t) cc_final: 0.9117 (t) REVERT: A 300 LYS cc_start: 0.8554 (mttt) cc_final: 0.7929 (tttm) REVERT: A 361 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8073 (tptp) REVERT: A 381 MET cc_start: 0.5123 (ttt) cc_final: 0.4608 (ttm) REVERT: A 409 MET cc_start: 0.7896 (ttt) cc_final: 0.7692 (mtp) REVERT: A 503 ARG cc_start: 0.8138 (mtm180) cc_final: 0.7730 (ptm160) REVERT: A 508 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8272 (mmtm) outliers start: 15 outliers final: 10 residues processed: 98 average time/residue: 0.1049 time to fit residues: 13.6733 Evaluate side-chains 93 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.0870 chunk 38 optimal weight: 9.9990 chunk 31 optimal weight: 0.0170 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3725 Z= 0.179 Angle : 0.571 6.524 5083 Z= 0.289 Chirality : 0.043 0.182 598 Planarity : 0.005 0.051 627 Dihedral : 4.455 22.410 501 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.75 % Allowed : 21.98 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.41), residues: 471 helix: 0.81 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.83 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.001 0.000 HIS A 146 PHE 0.031 0.001 PHE A 134 TYR 0.014 0.001 TYR A 55 ARG 0.001 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7138 (t0) cc_final: 0.6599 (t0) REVERT: A 164 CYS cc_start: 0.9344 (t) cc_final: 0.9126 (t) REVERT: A 300 LYS cc_start: 0.8553 (mttt) cc_final: 0.7927 (tttm) REVERT: A 361 LYS cc_start: 0.8632 (tmtt) cc_final: 0.8086 (tptp) REVERT: A 381 MET cc_start: 0.4951 (ttt) cc_final: 0.4433 (ttm) REVERT: A 466 GLN cc_start: 0.6739 (pt0) cc_final: 0.6323 (pp30) REVERT: A 503 ARG cc_start: 0.8145 (mtm180) cc_final: 0.7541 (ptm160) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.1076 time to fit residues: 14.4843 Evaluate side-chains 96 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3725 Z= 0.177 Angle : 0.569 7.079 5083 Z= 0.287 Chirality : 0.043 0.193 598 Planarity : 0.005 0.049 627 Dihedral : 4.398 22.418 501 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.22 % Allowed : 23.86 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.41), residues: 471 helix: 0.86 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -2.79 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 91 HIS 0.002 0.000 HIS A 146 PHE 0.032 0.001 PHE A 134 TYR 0.015 0.001 TYR A 55 ARG 0.001 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7084 (t0) cc_final: 0.6554 (t0) REVERT: A 164 CYS cc_start: 0.9345 (t) cc_final: 0.9142 (t) REVERT: A 300 LYS cc_start: 0.8561 (mttt) cc_final: 0.7948 (tttm) REVERT: A 361 LYS cc_start: 0.8579 (tmtt) cc_final: 0.8090 (tptp) REVERT: A 381 MET cc_start: 0.4945 (ttt) cc_final: 0.4422 (ttm) REVERT: A 466 GLN cc_start: 0.6738 (pt0) cc_final: 0.6215 (pp30) REVERT: A 508 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8272 (mmtm) outliers start: 12 outliers final: 10 residues processed: 99 average time/residue: 0.1071 time to fit residues: 14.0583 Evaluate side-chains 99 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3725 Z= 0.175 Angle : 0.575 7.235 5083 Z= 0.286 Chirality : 0.042 0.188 598 Planarity : 0.005 0.049 627 Dihedral : 4.335 22.376 501 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.22 % Allowed : 25.47 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.41), residues: 471 helix: 0.94 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -2.75 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.001 0.000 HIS A 146 PHE 0.032 0.001 PHE A 134 TYR 0.009 0.001 TYR A 55 ARG 0.001 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7094 (t0) cc_final: 0.6558 (t0) REVERT: A 300 LYS cc_start: 0.8587 (mttt) cc_final: 0.7972 (tttm) REVERT: A 334 GLN cc_start: 0.8010 (pt0) cc_final: 0.7589 (mt0) REVERT: A 361 LYS cc_start: 0.8520 (tmtt) cc_final: 0.8097 (tptp) REVERT: A 381 MET cc_start: 0.4889 (ttt) cc_final: 0.4359 (ttm) REVERT: A 466 GLN cc_start: 0.6525 (pt0) cc_final: 0.5999 (pp30) REVERT: A 503 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7763 (ptm160) REVERT: A 508 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8346 (mmtm) outliers start: 12 outliers final: 10 residues processed: 97 average time/residue: 0.1075 time to fit residues: 13.8267 Evaluate side-chains 98 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3725 Z= 0.226 Angle : 0.608 7.330 5083 Z= 0.305 Chirality : 0.044 0.201 598 Planarity : 0.005 0.049 627 Dihedral : 4.407 22.735 501 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.09 % Allowed : 24.66 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.41), residues: 471 helix: 1.01 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -2.83 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.002 0.001 HIS A 166 PHE 0.033 0.001 PHE A 134 TYR 0.009 0.001 TYR A 55 ARG 0.002 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7074 (t0) cc_final: 0.6540 (t0) REVERT: A 300 LYS cc_start: 0.8565 (mttt) cc_final: 0.7959 (tttm) REVERT: A 334 GLN cc_start: 0.8058 (pt0) cc_final: 0.7622 (mt0) REVERT: A 361 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8090 (tptp) REVERT: A 381 MET cc_start: 0.4946 (ttt) cc_final: 0.4423 (ttm) REVERT: A 466 GLN cc_start: 0.6538 (pt0) cc_final: 0.5969 (pp30) REVERT: A 503 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7780 (ptm160) REVERT: A 508 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8400 (mmtm) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.1083 time to fit residues: 14.0609 Evaluate side-chains 102 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3725 Z= 0.174 Angle : 0.599 9.356 5083 Z= 0.294 Chirality : 0.043 0.202 598 Planarity : 0.005 0.047 627 Dihedral : 4.333 22.519 501 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.95 % Allowed : 27.08 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.41), residues: 471 helix: 1.03 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -2.69 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 407 HIS 0.001 0.000 HIS A 166 PHE 0.033 0.001 PHE A 134 TYR 0.009 0.001 TYR A 55 ARG 0.002 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7074 (t0) cc_final: 0.6554 (t0) REVERT: A 300 LYS cc_start: 0.8590 (mttt) cc_final: 0.7966 (tttm) REVERT: A 334 GLN cc_start: 0.7974 (pt0) cc_final: 0.7546 (mt0) REVERT: A 361 LYS cc_start: 0.8423 (tmtt) cc_final: 0.8025 (tptp) REVERT: A 381 MET cc_start: 0.4931 (ttt) cc_final: 0.4398 (ttm) REVERT: A 466 GLN cc_start: 0.6508 (pt0) cc_final: 0.5937 (pp30) REVERT: A 503 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7777 (ptm160) REVERT: A 508 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8409 (mmtm) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.1051 time to fit residues: 14.4606 Evaluate side-chains 96 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3725 Z= 0.196 Angle : 0.623 11.824 5083 Z= 0.304 Chirality : 0.044 0.198 598 Planarity : 0.005 0.046 627 Dihedral : 4.325 22.831 501 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.95 % Allowed : 28.42 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.41), residues: 471 helix: 1.13 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -2.76 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 407 HIS 0.002 0.000 HIS A 166 PHE 0.033 0.002 PHE A 134 TYR 0.011 0.001 TYR A 55 ARG 0.002 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7021 (t0) cc_final: 0.6499 (t0) REVERT: A 300 LYS cc_start: 0.8591 (mttt) cc_final: 0.8015 (tttt) REVERT: A 334 GLN cc_start: 0.8006 (pt0) cc_final: 0.7594 (mt0) REVERT: A 361 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8033 (tptp) REVERT: A 381 MET cc_start: 0.4926 (ttt) cc_final: 0.4399 (ttm) REVERT: A 466 GLN cc_start: 0.6484 (pt0) cc_final: 0.5874 (pp30) REVERT: A 503 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7777 (ptm160) REVERT: A 508 LYS cc_start: 0.8755 (mmtm) cc_final: 0.8447 (mmtm) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.1063 time to fit residues: 13.9139 Evaluate side-chains 97 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101720 restraints weight = 7073.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105235 restraints weight = 3707.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107775 restraints weight = 2417.984| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3725 Z= 0.172 Angle : 0.618 12.050 5083 Z= 0.299 Chirality : 0.044 0.211 598 Planarity : 0.005 0.046 627 Dihedral : 4.297 22.647 501 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.41 % Allowed : 28.69 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.41), residues: 471 helix: 1.11 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -2.68 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 407 HIS 0.001 0.000 HIS A 166 PHE 0.032 0.001 PHE A 134 TYR 0.011 0.001 TYR A 55 ARG 0.002 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1101.08 seconds wall clock time: 20 minutes 32.62 seconds (1232.62 seconds total)