Starting phenix.real_space_refine on Mon Mar 11 10:28:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/03_2024/7kdt_22829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/03_2024/7kdt_22829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/03_2024/7kdt_22829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/03_2024/7kdt_22829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/03_2024/7kdt_22829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/03_2024/7kdt_22829.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.105 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 2543 2.51 5 N 683 2.21 5 O 769 1.98 5 H 4042 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 351": "OD1" <-> "OD2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8064 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7444 Classifications: {'peptide': 467} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 454} Chain breaks: 1 Chain: "B" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 620 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Time building chain proxies: 4.15, per 1000 atoms: 0.51 Number of scatterers: 8064 At special positions: 0 Unit cell: (57.546, 70.89, 115.926, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 769 8.00 N 683 7.00 C 2543 6.00 H 4042 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.64 Conformation dependent library (CDL) restraints added in 907.4 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 109 through 127 removed outlier: 4.286A pdb=" N ALA A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.708A pdb=" N ALA A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 221 through 245 removed outlier: 3.571A pdb=" N GLU A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 299 through 307 removed outlier: 4.360A pdb=" N GLN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.501A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 343 removed outlier: 6.115A pdb=" N GLU A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Proline residue: A 350 - end of helix removed outlier: 3.595A pdb=" N VAL A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.624A pdb=" N ALA A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.809A pdb=" N TYR A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.521A pdb=" N ALA A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 452 removed outlier: 3.653A pdb=" N GLN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 472 removed outlier: 3.816A pdb=" N GLU A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.514A pdb=" N GLU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 removed outlier: 4.136A pdb=" N TYR A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 removed outlier: 3.881A pdb=" N GLU A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 558 Processing helix chain 'A' and resid 560 through 573 Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.688A pdb=" N HIS A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 599 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 69 removed outlier: 4.876A pdb=" N SER B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 290 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 1022 1.06 - 1.25: 3587 1.25 - 1.44: 1110 1.44 - 1.63: 2367 1.63 - 1.82: 42 Bond restraints: 8128 Sorted by residual: bond pdb=" C GLN A 115 " pdb=" O GLN A 115 " ideal model delta sigma weight residual 1.236 1.141 0.095 1.15e-02 7.56e+03 6.85e+01 bond pdb=" N GLU A 549 " pdb=" H GLU A 549 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 TYR A 479 " pdb=" HD1 TYR A 479 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 PHE A 390 " pdb=" HD1 PHE A 390 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 TYR A 304 " pdb=" HD1 TYR A 304 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 8123 not shown) Histogram of bond angle deviations from ideal: 95.77 - 103.49: 54 103.49 - 111.21: 8481 111.21 - 118.93: 2963 118.93 - 126.65: 3194 126.65 - 134.37: 38 Bond angle restraints: 14730 Sorted by residual: angle pdb=" CA GLN A 115 " pdb=" C GLN A 115 " pdb=" O GLN A 115 " ideal model delta sigma weight residual 120.82 114.53 6.29 1.05e+00 9.07e-01 3.58e+01 angle pdb=" CA GLN A 132 " pdb=" C GLN A 132 " pdb=" O GLN A 132 " ideal model delta sigma weight residual 120.42 114.45 5.97 1.06e+00 8.90e-01 3.18e+01 angle pdb=" N GLN A 416 " pdb=" CA GLN A 416 " pdb=" C GLN A 416 " ideal model delta sigma weight residual 109.62 102.09 7.53 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C LYS A 516 " pdb=" N GLY A 517 " pdb=" CA GLY A 517 " ideal model delta sigma weight residual 119.94 125.39 -5.45 1.09e+00 8.42e-01 2.50e+01 angle pdb=" CA LYS A 349 " pdb=" C LYS A 349 " pdb=" O LYS A 349 " ideal model delta sigma weight residual 118.33 113.80 4.53 9.20e-01 1.18e+00 2.43e+01 ... (remaining 14725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3508 17.70 - 35.41: 182 35.41 - 53.11: 47 53.11 - 70.81: 47 70.81 - 88.52: 21 Dihedral angle restraints: 3805 sinusoidal: 2092 harmonic: 1713 Sorted by residual: dihedral pdb=" CA GLU A 320 " pdb=" C GLU A 320 " pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N ARG B 47 " pdb=" CA ARG B 47 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA THR A 451 " pdb=" C THR A 451 " pdb=" N GLY A 452 " pdb=" CA GLY A 452 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 3802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 342 0.063 - 0.127: 181 0.127 - 0.190: 51 0.190 - 0.253: 22 0.253 - 0.316: 6 Chirality restraints: 602 Sorted by residual: chirality pdb=" CA GLU A 308 " pdb=" N GLU A 308 " pdb=" C GLU A 308 " pdb=" CB GLU A 308 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA PHE A 219 " pdb=" N PHE A 219 " pdb=" C PHE A 219 " pdb=" CB PHE A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ARG A 529 " pdb=" N ARG A 529 " pdb=" C ARG A 529 " pdb=" CB ARG A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 599 not shown) Planarity restraints: 1201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 520 " 0.056 2.00e-02 2.50e+03 4.40e-01 2.91e+03 pdb=" CD GLN A 520 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN A 520 " -0.052 2.00e-02 2.50e+03 pdb=" NE2 GLN A 520 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 520 " 0.768 2.00e-02 2.50e+03 pdb="HE22 GLN A 520 " -0.754 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 115 " 0.078 2.00e-02 2.50e+03 4.36e-01 2.85e+03 pdb=" CD GLN A 115 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN A 115 " -0.084 2.00e-02 2.50e+03 pdb=" NE2 GLN A 115 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 115 " -0.753 2.00e-02 2.50e+03 pdb="HE22 GLN A 115 " 0.748 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 220 " 0.119 2.00e-02 2.50e+03 4.33e-01 2.82e+03 pdb=" CD GLN A 220 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 220 " -0.115 2.00e-02 2.50e+03 pdb=" NE2 GLN A 220 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 220 " 0.745 2.00e-02 2.50e+03 pdb="HE22 GLN A 220 " -0.738 2.00e-02 2.50e+03 ... (remaining 1198 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 413 2.20 - 2.80: 15423 2.80 - 3.40: 23181 3.40 - 4.00: 29503 4.00 - 4.60: 44103 Nonbonded interactions: 112623 Sorted by model distance: nonbonded pdb=" OD2 ASP A 267 " pdb=" HG SER A 270 " model vdw 1.603 1.850 nonbonded pdb=" OE1 GLU A 217 " pdb=" HG SER A 224 " model vdw 1.611 1.850 nonbonded pdb=" OD1 ASP A 151 " pdb=" HG SER A 153 " model vdw 1.625 1.850 nonbonded pdb=" O ALA A 483 " pdb=" HG1 THR A 487 " model vdw 1.654 1.850 nonbonded pdb=" OD1 ASN A 509 " pdb=" HG1 THR A 512 " model vdw 1.663 1.850 ... (remaining 112618 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: 0.700 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: 0.130 Extract box with map and model: 4.030 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.012 0.095 4086 Z= 0.778 Angle : 1.742 7.528 5493 Z= 1.206 Chirality : 0.088 0.316 602 Planarity : 0.018 0.193 714 Dihedral : 14.556 88.516 1574 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.47 % Allowed : 1.17 % Favored : 98.37 % 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: -1.64 (0.32), residues: 499 helix: -0.92 (0.21), residues: 405 sheet: None (None), residues: 0 loop : -0.95 (0.65), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.018 TRP A 523 HIS 0.012 0.004 HIS A 405 PHE 0.070 0.015 PHE A 191 TYR 0.171 0.021 TYR A 186 ARG 0.009 0.002 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8506 (tttp) cc_final: 0.8177 (mtpt) outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.4468 time to fit residues: 65.2371 Evaluate side-chains 72 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 515 HIS A 520 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4086 Z= 0.193 Angle : 0.585 5.673 5493 Z= 0.322 Chirality : 0.035 0.129 602 Planarity : 0.004 0.054 714 Dihedral : 4.956 23.668 542 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.93 % Allowed : 7.23 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.36), residues: 499 helix: 1.00 (0.24), residues: 412 sheet: None (None), residues: 0 loop : -0.72 (0.62), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 169 HIS 0.004 0.002 HIS A 583 PHE 0.020 0.002 PHE A 465 TYR 0.023 0.002 TYR A 186 ARG 0.004 0.001 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8417 (tttp) cc_final: 0.8186 (mtpt) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.3346 time to fit residues: 35.2308 Evaluate side-chains 70 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.7800 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4086 Z= 0.250 Angle : 0.540 4.586 5493 Z= 0.297 Chirality : 0.035 0.123 602 Planarity : 0.004 0.045 714 Dihedral : 4.535 20.667 542 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 8.62 % Favored : 89.98 % 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: 1.38 (0.36), residues: 499 helix: 1.28 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -0.60 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.006 0.002 HIS A 515 PHE 0.019 0.002 PHE A 163 TYR 0.014 0.001 TYR A 186 ARG 0.003 0.001 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.3864 time to fit residues: 32.7969 Evaluate side-chains 62 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4086 Z= 0.275 Angle : 0.536 5.814 5493 Z= 0.295 Chirality : 0.035 0.123 602 Planarity : 0.004 0.036 714 Dihedral : 4.466 19.573 542 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.17 % Allowed : 10.02 % Favored : 88.81 % 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: 1.51 (0.36), residues: 499 helix: 1.36 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.56 (0.70), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 169 HIS 0.005 0.002 HIS A 405 PHE 0.018 0.002 PHE A 163 TYR 0.015 0.001 TYR A 377 ARG 0.002 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.3663 time to fit residues: 30.9668 Evaluate side-chains 62 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4086 Z= 0.244 Angle : 0.508 4.653 5493 Z= 0.278 Chirality : 0.034 0.123 602 Planarity : 0.004 0.037 714 Dihedral : 4.298 18.690 542 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.86 % Allowed : 10.72 % Favored : 87.41 % 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: 1.80 (0.37), residues: 499 helix: 1.56 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.50 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 169 HIS 0.005 0.002 HIS A 515 PHE 0.016 0.001 PHE A 338 TYR 0.014 0.001 TYR A 377 ARG 0.001 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8120 (mm-30) REVERT: A 271 GLN cc_start: 0.7511 (mt0) cc_final: 0.7284 (mt0) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.3172 time to fit residues: 27.1388 Evaluate side-chains 63 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.7878 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4086 Z= 0.304 Angle : 0.529 4.419 5493 Z= 0.293 Chirality : 0.035 0.125 602 Planarity : 0.004 0.038 714 Dihedral : 4.357 18.167 542 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.56 % Allowed : 10.02 % Favored : 87.41 % 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: 1.61 (0.36), residues: 499 helix: 1.49 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -0.76 (0.68), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 169 HIS 0.006 0.002 HIS A 515 PHE 0.017 0.002 PHE A 338 TYR 0.017 0.002 TYR A 377 ARG 0.002 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8109 (mm-30) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.4171 time to fit residues: 35.0435 Evaluate side-chains 63 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4086 Z= 0.152 Angle : 0.463 4.368 5493 Z= 0.249 Chirality : 0.032 0.112 602 Planarity : 0.003 0.038 714 Dihedral : 4.087 17.927 542 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.40 % Allowed : 10.96 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.38), residues: 499 helix: 2.04 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.54 (0.70), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 169 HIS 0.003 0.001 HIS A 406 PHE 0.014 0.001 PHE A 338 TYR 0.009 0.001 TYR A 450 ARG 0.001 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.3944 time to fit residues: 32.1149 Evaluate side-chains 61 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4086 Z= 0.198 Angle : 0.479 4.352 5493 Z= 0.260 Chirality : 0.033 0.119 602 Planarity : 0.003 0.036 714 Dihedral : 4.046 17.898 542 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.63 % Allowed : 10.49 % Favored : 87.88 % 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: 2.44 (0.37), residues: 499 helix: 2.09 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.67 (0.68), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 169 HIS 0.004 0.001 HIS A 515 PHE 0.014 0.001 PHE A 338 TYR 0.011 0.001 TYR A 377 ARG 0.001 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 MET cc_start: 0.7767 (mmt) cc_final: 0.5849 (mmt) outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 0.4222 time to fit residues: 33.8675 Evaluate side-chains 62 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7768 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4086 Z= 0.142 Angle : 0.459 4.413 5493 Z= 0.243 Chirality : 0.032 0.116 602 Planarity : 0.003 0.036 714 Dihedral : 3.868 17.475 542 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.70 % Allowed : 11.66 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.38), residues: 499 helix: 2.42 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.54 (0.67), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 169 HIS 0.003 0.001 HIS A 406 PHE 0.012 0.001 PHE A 338 TYR 0.008 0.001 TYR A 450 ARG 0.002 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 561 MET cc_start: 0.7732 (mmt) cc_final: 0.5916 (mmt) outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.4012 time to fit residues: 30.3827 Evaluate side-chains 59 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 488 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4086 Z= 0.137 Angle : 0.450 4.555 5493 Z= 0.238 Chirality : 0.031 0.116 602 Planarity : 0.003 0.037 714 Dihedral : 3.723 17.527 542 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.47 % Allowed : 12.12 % Favored : 87.41 % 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: 3.10 (0.38), residues: 499 helix: 2.56 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.55 (0.66), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 169 HIS 0.002 0.001 HIS A 406 PHE 0.011 0.001 PHE A 338 TYR 0.007 0.001 TYR A 450 ARG 0.001 0.000 ARG A 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 MET cc_start: 0.7751 (mmt) cc_final: 0.5998 (mmt) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.4082 time to fit residues: 31.0074 Evaluate side-chains 56 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.148569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122658 restraints weight = 16261.023| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.71 r_work: 0.3492 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4086 Z= 0.175 Angle : 0.466 4.329 5493 Z= 0.249 Chirality : 0.032 0.115 602 Planarity : 0.003 0.036 714 Dihedral : 3.779 16.947 542 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.70 % Allowed : 12.12 % Favored : 87.18 % 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: 2.92 (0.37), residues: 499 helix: 2.42 (0.25), residues: 413 sheet: None (None), residues: 0 loop : -0.53 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 169 HIS 0.003 0.001 HIS A 515 PHE 0.013 0.001 PHE A 338 TYR 0.009 0.001 TYR A 377 ARG 0.001 0.000 ARG A 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2611.38 seconds wall clock time: 46 minutes 36.09 seconds (2796.09 seconds total)