Starting phenix.real_space_refine on Wed Jan 17 16:22:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yim_33861/01_2024/7yim_33861.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yim_33861/01_2024/7yim_33861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yim_33861/01_2024/7yim_33861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yim_33861/01_2024/7yim_33861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yim_33861/01_2024/7yim_33861.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yim_33861/01_2024/7yim_33861.pdb" } resolution = 2.6 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= -0.006 sd= 0.095 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 40 5.16 5 C 2925 2.51 5 N 791 2.21 5 O 901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4657 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4657 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 570} Time building chain proxies: 2.91, per 1000 atoms: 0.62 Number of scatterers: 4657 At special positions: 0 Unit cell: (69.5594, 91.3616, 103.82, 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 40 16.00 O 901 8.00 N 791 7.00 C 2925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 124 " distance=2.02 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.01 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.00 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.01 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.01 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.01 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " 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: 1.74 Conformation dependent library (CDL) restraints added in 836.4 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 4.209A pdb=" N ASP A 33 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.750A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 removed outlier: 3.573A pdb=" N GLU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.546A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.613A pdb=" N SER A 115 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 116 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.629A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 174 through 193 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 197 through 231 removed outlier: 3.915A pdb=" N THR A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 251 through 271 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.018A pdb=" N LEU A 305 " --> pdb=" O CYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 343 through 361 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.746A pdb=" N PHE A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 4.181A pdb=" N CYS A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 439 removed outlier: 7.982A pdb=" N GLU A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N TYR A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.204A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.527A pdb=" N GLY A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.999A pdb=" N LYS A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 Processing helix chain 'A' and resid 565 through 582 Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.913A pdb=" N CYS A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 924 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: 1.26 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1072 1.33 - 1.46: 1193 1.46 - 1.58: 2428 1.58 - 1.71: 0 1.71 - 1.84: 48 Bond restraints: 4741 Sorted by residual: bond pdb=" CB VAL A 355 " pdb=" CG2 VAL A 355 " ideal model delta sigma weight residual 1.521 1.408 0.113 3.30e-02 9.18e+02 1.17e+01 bond pdb=" C TYR A 174 " pdb=" N ALA A 175 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.09e-02 8.42e+03 1.04e+01 bond pdb=" CG GLN A 245 " pdb=" CD GLN A 245 " ideal model delta sigma weight residual 1.516 1.439 0.077 2.50e-02 1.60e+03 9.56e+00 bond pdb=" CB GLN A 245 " pdb=" CG GLN A 245 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.55e+00 bond pdb=" CG1 ILE A 314 " pdb=" CD1 ILE A 314 " ideal model delta sigma weight residual 1.513 1.400 0.113 3.90e-02 6.57e+02 8.40e+00 ... (remaining 4736 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.32: 75 105.32 - 112.55: 2337 112.55 - 119.78: 1897 119.78 - 127.01: 2053 127.01 - 134.24: 38 Bond angle restraints: 6400 Sorted by residual: angle pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " ideal model delta sigma weight residual 114.40 128.76 -14.36 2.30e+00 1.89e-01 3.90e+01 angle pdb=" C CYS A 591 " pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sigma weight residual 110.88 103.82 7.06 1.57e+00 4.06e-01 2.02e+01 angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sigma weight residual 114.10 122.78 -8.68 2.00e+00 2.50e-01 1.88e+01 angle pdb=" C GLU A 398 " pdb=" N GLU A 399 " pdb=" CA GLU A 399 " ideal model delta sigma weight residual 122.60 116.29 6.31 1.56e+00 4.11e-01 1.64e+01 angle pdb=" C LYS A 581 " pdb=" N CYS A 582 " pdb=" CA CYS A 582 " ideal model delta sigma weight residual 122.54 115.64 6.90 1.82e+00 3.02e-01 1.44e+01 ... (remaining 6395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 2536 17.11 - 34.21: 342 34.21 - 51.31: 60 51.31 - 68.42: 19 68.42 - 85.52: 5 Dihedral angle restraints: 2962 sinusoidal: 1222 harmonic: 1740 Sorted by residual: dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual 93.00 173.66 -80.66 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA LYS A 76 " pdb=" C LYS A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta harmonic sigma weight residual -180.00 -144.61 -35.39 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA SER A 117 " pdb=" C SER A 117 " pdb=" N GLU A 118 " pdb=" CA GLU A 118 " ideal model delta harmonic sigma weight residual -180.00 -146.39 -33.61 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 519 0.070 - 0.139: 176 0.139 - 0.209: 19 0.209 - 0.278: 4 0.278 - 0.348: 1 Chirality restraints: 719 Sorted by residual: chirality pdb=" CB ILE A 481 " pdb=" CA ILE A 481 " pdb=" CG1 ILE A 481 " pdb=" CG2 ILE A 481 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB VAL A 355 " pdb=" CA VAL A 355 " pdb=" CG1 VAL A 355 " pdb=" CG2 VAL A 355 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO A 510 " pdb=" N PRO A 510 " pdb=" C PRO A 510 " pdb=" CB PRO A 510 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 716 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO A 510 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 592 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C PHE A 592 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE A 592 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 593 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 175 " 0.045 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 176 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.038 5.00e-02 4.00e+02 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1194 2.80 - 3.32: 4406 3.32 - 3.85: 7985 3.85 - 4.37: 9276 4.37 - 4.90: 15248 Nonbonded interactions: 38109 Sorted by model distance: nonbonded pdb=" OE1 GLU A 165 " pdb=" NH1 ARG A 169 " model vdw 2.272 2.520 nonbonded pdb=" O ARG A 509 " pdb=" OG SER A 513 " model vdw 2.276 2.440 nonbonded pdb=" OE1 GLU A 62 " pdb=" OH TYR A 108 " model vdw 2.284 2.440 nonbonded pdb=" OG SER A 42 " pdb=" OD2 ASP A 45 " model vdw 2.294 2.440 nonbonded pdb=" O ALA A 44 " pdb=" OG1 THR A 48 " model vdw 2.311 2.440 ... (remaining 38104 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.000 Extract box with map and model: 0.990 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.910 Find NCS groups from input model: 0.130 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 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 : 0.013 0.113 4741 Z= 0.829 Angle : 1.136 14.355 6400 Z= 0.635 Chirality : 0.068 0.348 719 Planarity : 0.009 0.089 837 Dihedral : 15.893 85.522 1782 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.78 % Allowed : 6.59 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.25), residues: 590 helix: -2.57 (0.18), residues: 420 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.007 TRP A 181 HIS 0.012 0.003 HIS A 483 PHE 0.031 0.005 PHE A 235 TYR 0.043 0.005 TYR A 185 ARG 0.008 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 519 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6959 (tm-30) outliers start: 4 outliers final: 0 residues processed: 68 average time/residue: 1.5274 time to fit residues: 107.4513 Evaluate side-chains 37 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 28 optimal weight: 0.0030 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 116 GLN A 220 ASN A 389 ASN A 420 GLN A 534 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4741 Z= 0.186 Angle : 0.554 7.343 6400 Z= 0.300 Chirality : 0.039 0.157 719 Planarity : 0.005 0.050 837 Dihedral : 5.211 29.794 631 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.97 % Allowed : 13.76 % Favored : 85.27 % 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: -1.46 (0.31), residues: 590 helix: -0.37 (0.23), residues: 429 sheet: None (None), residues: 0 loop : -2.36 (0.42), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 181 HIS 0.006 0.001 HIS A 534 PHE 0.016 0.001 PHE A 235 TYR 0.015 0.001 TYR A 185 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6611 (tp) cc_final: 0.6326 (tp) outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 1.2522 time to fit residues: 79.6367 Evaluate side-chains 44 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.0270 chunk 18 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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: 0.6351 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4741 Z= 0.179 Angle : 0.536 7.940 6400 Z= 0.283 Chirality : 0.039 0.145 719 Planarity : 0.004 0.040 837 Dihedral : 4.657 26.109 631 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.55 % Allowed : 15.89 % Favored : 82.56 % 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: -0.34 (0.33), residues: 590 helix: 0.51 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -2.19 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.025 0.002 PHE A 50 TYR 0.013 0.001 TYR A 185 ARG 0.008 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.561 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.9983 time to fit residues: 55.8730 Evaluate side-chains 38 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 28 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4741 Z= 0.173 Angle : 0.509 7.025 6400 Z= 0.271 Chirality : 0.039 0.131 719 Planarity : 0.004 0.037 837 Dihedral : 4.383 22.705 631 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.33 % Allowed : 16.09 % Favored : 81.59 % 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: 0.20 (0.34), residues: 590 helix: 0.89 (0.24), residues: 433 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 483 PHE 0.029 0.002 PHE A 50 TYR 0.009 0.001 TYR A 185 ARG 0.004 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLN cc_start: 0.5434 (OUTLIER) cc_final: 0.5178 (mt0) REVERT: A 530 LYS cc_start: 0.6005 (mtmt) cc_final: 0.5693 (mtmp) REVERT: A 534 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.6512 (p90) outliers start: 12 outliers final: 2 residues processed: 53 average time/residue: 1.0764 time to fit residues: 60.1149 Evaluate side-chains 40 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.6405 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4741 Z= 0.227 Angle : 0.548 7.727 6400 Z= 0.292 Chirality : 0.041 0.135 719 Planarity : 0.004 0.041 837 Dihedral : 4.411 21.472 631 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.10 % Allowed : 17.83 % Favored : 79.07 % 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 (0.34), residues: 590 helix: 0.93 (0.24), residues: 426 sheet: None (None), residues: 0 loop : -1.84 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.029 0.002 PHE A 54 TYR 0.011 0.001 TYR A 185 ARG 0.003 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLN cc_start: 0.5556 (OUTLIER) cc_final: 0.5308 (mt0) REVERT: A 403 LYS cc_start: 0.6751 (pttt) cc_final: 0.6382 (tptp) REVERT: A 530 LYS cc_start: 0.5979 (mtmt) cc_final: 0.5602 (mtmp) REVERT: A 534 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.6375 (p90) outliers start: 16 outliers final: 7 residues processed: 55 average time/residue: 1.0340 time to fit residues: 60.0355 Evaluate side-chains 47 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4741 Z= 0.220 Angle : 0.558 8.399 6400 Z= 0.294 Chirality : 0.041 0.143 719 Planarity : 0.004 0.040 837 Dihedral : 4.475 20.609 631 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.13 % Allowed : 19.77 % Favored : 78.10 % 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: 0.50 (0.34), residues: 590 helix: 1.05 (0.24), residues: 426 sheet: None (None), residues: 0 loop : -1.52 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.023 0.002 PHE A 50 TYR 0.011 0.001 TYR A 185 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 291 GLN cc_start: 0.5498 (OUTLIER) cc_final: 0.5254 (mt0) REVERT: A 403 LYS cc_start: 0.6801 (pttt) cc_final: 0.6490 (tptp) REVERT: A 530 LYS cc_start: 0.5962 (mtmt) cc_final: 0.5600 (mtmp) REVERT: A 534 HIS cc_start: 0.6890 (OUTLIER) cc_final: 0.6504 (p90) outliers start: 11 outliers final: 8 residues processed: 46 average time/residue: 1.0652 time to fit residues: 51.6979 Evaluate side-chains 49 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.6383 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4741 Z= 0.201 Angle : 0.544 9.026 6400 Z= 0.289 Chirality : 0.040 0.131 719 Planarity : 0.004 0.039 837 Dihedral : 4.373 20.101 631 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.13 % Allowed : 20.35 % Favored : 77.52 % 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: 0.65 (0.34), residues: 590 helix: 1.19 (0.24), residues: 424 sheet: None (None), residues: 0 loop : -1.53 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.021 0.002 PHE A 54 TYR 0.015 0.001 TYR A 151 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 403 LYS cc_start: 0.6712 (pttt) cc_final: 0.6511 (tptp) REVERT: A 530 LYS cc_start: 0.6048 (mtmt) cc_final: 0.5707 (mtmp) REVERT: A 534 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6237 (p90) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 1.0010 time to fit residues: 46.5896 Evaluate side-chains 44 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.0020 chunk 28 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5306 ------------------------------------------------------------------------------- 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: 0.6319 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4741 Z= 0.170 Angle : 0.515 9.957 6400 Z= 0.274 Chirality : 0.038 0.125 719 Planarity : 0.004 0.037 837 Dihedral : 4.109 19.675 631 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.71 % Allowed : 20.16 % Favored : 77.13 % 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: 1.08 (0.34), residues: 590 helix: 1.51 (0.25), residues: 424 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 483 PHE 0.020 0.002 PHE A 54 TYR 0.013 0.001 TYR A 151 ARG 0.001 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.502 Fit side-chains REVERT: A 530 LYS cc_start: 0.5988 (mtmt) cc_final: 0.5588 (mtmp) REVERT: A 534 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6237 (p90) outliers start: 14 outliers final: 5 residues processed: 52 average time/residue: 1.0629 time to fit residues: 58.1820 Evaluate side-chains 41 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.6358 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4741 Z= 0.200 Angle : 0.569 10.418 6400 Z= 0.302 Chirality : 0.040 0.127 719 Planarity : 0.004 0.037 837 Dihedral : 4.127 19.322 631 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.94 % Allowed : 21.51 % Favored : 76.55 % 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: 1.00 (0.34), residues: 590 helix: 1.45 (0.24), residues: 424 sheet: None (None), residues: 0 loop : -1.39 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.025 0.002 PHE A 54 TYR 0.013 0.001 TYR A 151 ARG 0.001 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.545 Fit side-chains REVERT: A 534 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6217 (p90) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 1.0700 time to fit residues: 49.6536 Evaluate side-chains 41 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 0.0010 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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: 0.6323 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4741 Z= 0.180 Angle : 0.559 10.587 6400 Z= 0.297 Chirality : 0.039 0.133 719 Planarity : 0.004 0.036 837 Dihedral : 4.001 19.337 631 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.36 % Allowed : 22.48 % Favored : 76.16 % 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: 1.33 (0.34), residues: 590 helix: 1.76 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 483 PHE 0.025 0.002 PHE A 54 TYR 0.018 0.001 TYR A 164 ARG 0.004 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.493 Fit side-chains REVERT: A 124 CYS cc_start: 0.5810 (t) cc_final: 0.5387 (t) REVERT: A 490 MET cc_start: 0.6072 (mpt) cc_final: 0.5324 (mpt) REVERT: A 534 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6285 (p90) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.9889 time to fit residues: 47.0904 Evaluate side-chains 40 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4823 r_free = 0.4823 target = 0.208643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.163678 restraints weight = 5391.039| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.46 r_work: 0.4276 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4741 Z= 0.185 Angle : 0.564 10.588 6400 Z= 0.298 Chirality : 0.039 0.147 719 Planarity : 0.004 0.037 837 Dihedral : 4.003 18.564 631 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.36 % Allowed : 22.87 % Favored : 75.78 % 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: 1.30 (0.34), residues: 590 helix: 1.70 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -1.27 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.005 0.001 HIS A 483 PHE 0.027 0.002 PHE A 54 TYR 0.015 0.001 TYR A 151 ARG 0.006 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.54 seconds wall clock time: 32 minutes 28.52 seconds (1948.52 seconds total)