Starting phenix.real_space_refine on Thu Mar 6 06:48:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dnm_47042/03_2025/9dnm_47042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dnm_47042/03_2025/9dnm_47042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dnm_47042/03_2025/9dnm_47042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dnm_47042/03_2025/9dnm_47042.map" model { file = "/net/cci-nas-00/data/ceres_data/9dnm_47042/03_2025/9dnm_47042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dnm_47042/03_2025/9dnm_47042.cif" } resolution = 3.47 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= 0.010 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 18 5.16 5 C 3332 2.51 5 N 880 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5235 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3420 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'ODN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.20, per 1000 atoms: 0.80 Number of scatterers: 5235 At special positions: 0 Unit cell: (62.208, 110.592, 110.592, 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 18 16.00 O 1005 8.00 N 880 7.00 C 3332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.20 Conformation dependent library (CDL) restraints added in 610.6 milliseconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1262 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 11 sheets defined 19.9% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.515A pdb=" N ASP H 34 " --> pdb=" O ASN H 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.992A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 177 through 195 Processing helix chain 'A' and resid 198 through 219 removed outlier: 3.791A pdb=" N VAL A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.836A pdb=" N GLU A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 258 removed outlier: 3.565A pdb=" N PHE A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 269 through 282 removed outlier: 4.078A pdb=" N THR A 273 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.058A pdb=" N ASN A 381 " --> pdb=" O PHE A 378 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.987A pdb=" N ILE A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 416 " --> pdb=" O ARG A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.739A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.501A pdb=" N VAL H 123 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.506A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 11 through 13 removed outlier: 7.046A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.997A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 112 through 114 removed outlier: 6.193A pdb=" N VAL A 8 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 85 removed outlier: 6.624A pdb=" N CYS A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 168 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA9, first strand: chain 'A' and resid 284 through 289 removed outlier: 3.529A pdb=" N LEU A 300 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 299 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 308 through 310 Processing sheet with id=AB2, first strand: chain 'A' and resid 351 through 357 removed outlier: 5.479A pdb=" N LYS A 351 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA A 340 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN A 338 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 355 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 331 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A 444 " --> pdb=" O LEU A 428 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 564 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: 1.76 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1438 1.33 - 1.45: 874 1.45 - 1.57: 3012 1.57 - 1.69: 1 1.69 - 1.81: 25 Bond restraints: 5350 Sorted by residual: bond pdb=" N ASP A 35 " pdb=" CA ASP A 35 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 5.99e+00 bond pdb=" N MET A 453 " pdb=" CA MET A 453 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.53e-02 4.27e+03 4.84e+00 bond pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta sigma weight residual 1.462 1.490 -0.027 1.31e-02 5.83e+03 4.33e+00 bond pdb=" N HIS A 454 " pdb=" CA HIS A 454 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.79e-02 3.12e+03 4.01e+00 bond pdb=" C ASP A 35 " pdb=" N PRO A 36 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.22e-02 6.72e+03 2.65e+00 ... (remaining 5345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 7003 1.40 - 2.81: 215 2.81 - 4.21: 39 4.21 - 5.61: 10 5.61 - 7.01: 6 Bond angle restraints: 7273 Sorted by residual: angle pdb=" CB LYS A 330 " pdb=" CG LYS A 330 " pdb=" CD LYS A 330 " ideal model delta sigma weight residual 111.30 118.31 -7.01 2.30e+00 1.89e-01 9.30e+00 angle pdb=" CA LYS A 330 " pdb=" CB LYS A 330 " pdb=" CG LYS A 330 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.04e+00 angle pdb=" N PRO A 124 " pdb=" CA PRO A 124 " pdb=" C PRO A 124 " ideal model delta sigma weight residual 112.47 118.50 -6.03 2.06e+00 2.36e-01 8.57e+00 angle pdb=" CB GLU A 447 " pdb=" CG GLU A 447 " pdb=" CD GLU A 447 " ideal model delta sigma weight residual 112.60 117.20 -4.60 1.70e+00 3.46e-01 7.34e+00 angle pdb=" N LEU A 48 " pdb=" CA LEU A 48 " pdb=" C LEU A 48 " ideal model delta sigma weight residual 112.72 109.08 3.64 1.36e+00 5.41e-01 7.17e+00 ... (remaining 7268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 3006 21.51 - 43.03: 254 43.03 - 64.54: 37 64.54 - 86.06: 10 86.06 - 107.57: 3 Dihedral angle restraints: 3310 sinusoidal: 1358 harmonic: 1952 Sorted by residual: dihedral pdb=" CA PHE A 378 " pdb=" C PHE A 378 " pdb=" N LEU A 379 " pdb=" CA LEU A 379 " ideal model delta harmonic sigma weight residual 180.00 -159.51 -20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C2 ODN A 501 " pdb=" C ODN A 501 " pdb=" C1 ODN A 501 " pdb=" C7 ODN A 501 " ideal model delta sinusoidal sigma weight residual -53.57 54.00 -107.57 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O ODN A 501 " pdb=" C ODN A 501 " pdb=" C1 ODN A 501 " pdb=" C2 ODN A 501 " ideal model delta sinusoidal sigma weight residual 176.40 69.14 107.26 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 3307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 605 0.043 - 0.085: 153 0.085 - 0.128: 62 0.128 - 0.171: 3 0.171 - 0.213: 2 Chirality restraints: 825 Sorted by residual: chirality pdb=" CA LEU A 48 " pdb=" N LEU A 48 " pdb=" C LEU A 48 " pdb=" CB LEU A 48 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PRO A 124 " pdb=" N PRO A 124 " pdb=" C PRO A 124 " pdb=" CB PRO A 124 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA HIS A 454 " pdb=" N HIS A 454 " pdb=" C HIS A 454 " pdb=" CB HIS A 454 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 822 not shown) Planarity restraints: 927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 228 " 0.062 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO A 229 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 123 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 124 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 80 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO L 81 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO L 81 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 81 " 0.025 5.00e-02 4.00e+02 ... (remaining 924 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 769 2.76 - 3.29: 4660 3.29 - 3.83: 8111 3.83 - 4.36: 9086 4.36 - 4.90: 16474 Nonbonded interactions: 39100 Sorted by model distance: nonbonded pdb=" OD2 ASP A 305 " pdb=" OG SER A 316 " model vdw 2.222 3.040 nonbonded pdb=" NH1 ARG A 408 " pdb=" O ALA A 411 " model vdw 2.270 3.120 nonbonded pdb=" O LYS A 271 " pdb=" ND2 ASN A 275 " model vdw 2.271 3.120 nonbonded pdb=" OD2 ASP A 26 " pdb=" NH2 ARG A 169 " model vdw 2.296 3.120 nonbonded pdb=" O PHE A 291 " pdb=" OG SER A 294 " model vdw 2.329 3.040 ... (remaining 39095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.700 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.540 Find NCS groups from input model: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5350 Z= 0.276 Angle : 0.627 7.013 7273 Z= 0.330 Chirality : 0.044 0.213 825 Planarity : 0.006 0.094 927 Dihedral : 16.429 107.571 2042 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.18 % Allowed : 21.27 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.32 (0.34), residues: 654 helix: 2.36 (0.53), residues: 99 sheet: -0.11 (0.34), residues: 248 loop : -1.16 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.001 0.001 HIS A 30 PHE 0.016 0.002 PHE A 450 TYR 0.016 0.001 TYR L 92 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 10 SER cc_start: 0.8200 (m) cc_final: 0.7933 (t) REVERT: A 268 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6494 (mp0) REVERT: A 330 LYS cc_start: 0.7568 (tppt) cc_final: 0.7273 (tppt) REVERT: A 361 ASP cc_start: 0.6662 (m-30) cc_final: 0.6392 (m-30) REVERT: A 367 SER cc_start: 0.8665 (t) cc_final: 0.8442 (p) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2292 time to fit residues: 35.3822 Evaluate side-chains 124 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0070 chunk 37 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 overall best weight: 0.1774 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.130989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111226 restraints weight = 7821.934| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.71 r_work: 0.3220 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5350 Z= 0.170 Angle : 0.572 6.765 7273 Z= 0.296 Chirality : 0.043 0.139 825 Planarity : 0.005 0.070 927 Dihedral : 4.751 19.209 808 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.51 % Allowed : 18.63 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.02 (0.34), residues: 654 helix: 2.66 (0.52), residues: 99 sheet: 0.23 (0.33), residues: 249 loop : -1.07 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 111 HIS 0.002 0.000 HIS A 30 PHE 0.017 0.002 PHE A 117 TYR 0.011 0.001 TYR H 53 ARG 0.002 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: L 10 SER cc_start: 0.8261 (m) cc_final: 0.7966 (t) REVERT: A 57 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7448 (tp) REVERT: A 77 LYS cc_start: 0.8432 (mtpp) cc_final: 0.7982 (mtmm) REVERT: A 227 LYS cc_start: 0.6870 (mppt) cc_final: 0.6637 (mppt) REVERT: A 268 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6735 (mp0) REVERT: A 301 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6778 (tt0) REVERT: A 367 SER cc_start: 0.8735 (t) cc_final: 0.8161 (p) REVERT: A 386 ARG cc_start: 0.7102 (ttm110) cc_final: 0.6205 (ttm110) outliers start: 20 outliers final: 8 residues processed: 135 average time/residue: 0.2296 time to fit residues: 37.6499 Evaluate side-chains 123 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 269 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107214 restraints weight = 7941.160| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.70 r_work: 0.3167 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 5350 Z= 0.383 Angle : 0.664 7.475 7273 Z= 0.348 Chirality : 0.045 0.205 825 Planarity : 0.006 0.062 927 Dihedral : 5.025 19.811 808 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.22 % Allowed : 19.86 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.09 (0.33), residues: 654 helix: 2.58 (0.51), residues: 99 sheet: 0.33 (0.33), residues: 255 loop : -1.34 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 111 HIS 0.003 0.001 HIS H 38 PHE 0.029 0.003 PHE A 87 TYR 0.021 0.002 TYR H 53 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: H 94 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8737 (p) REVERT: H 101 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.7773 (ttt180) REVERT: L 10 SER cc_start: 0.8336 (m) cc_final: 0.8005 (t) REVERT: A 59 CYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7143 (t) REVERT: A 268 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6638 (mp0) REVERT: A 274 ARG cc_start: 0.8293 (tpt170) cc_final: 0.7757 (tpp-160) REVERT: A 275 ASN cc_start: 0.8499 (m-40) cc_final: 0.8027 (m110) REVERT: A 330 LYS cc_start: 0.7799 (tppt) cc_final: 0.7558 (tptp) REVERT: A 367 SER cc_start: 0.8754 (t) cc_final: 0.8180 (p) outliers start: 24 outliers final: 19 residues processed: 138 average time/residue: 0.2590 time to fit residues: 44.4546 Evaluate side-chains 145 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 21 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 17 optimal weight: 0.0570 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 11 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110010 restraints weight = 8105.886| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.63 r_work: 0.3217 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5350 Z= 0.166 Angle : 0.558 5.826 7273 Z= 0.291 Chirality : 0.042 0.148 825 Planarity : 0.005 0.057 927 Dihedral : 4.473 19.081 808 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.64 % Allowed : 22.14 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.19 (0.34), residues: 654 helix: 2.75 (0.52), residues: 100 sheet: 0.56 (0.33), residues: 255 loop : -1.20 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 111 HIS 0.001 0.000 HIS A 30 PHE 0.031 0.002 PHE A 87 TYR 0.011 0.001 TYR H 53 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 10 SER cc_start: 0.8326 (m) cc_final: 0.7986 (t) REVERT: A 57 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7543 (tp) REVERT: A 268 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6633 (mp0) REVERT: A 367 SER cc_start: 0.8749 (t) cc_final: 0.8152 (p) outliers start: 15 outliers final: 10 residues processed: 125 average time/residue: 0.2559 time to fit residues: 39.3541 Evaluate side-chains 125 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 291 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 0.0070 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110849 restraints weight = 7991.446| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.66 r_work: 0.3202 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5350 Z= 0.249 Angle : 0.584 5.963 7273 Z= 0.304 Chirality : 0.043 0.167 825 Planarity : 0.005 0.054 927 Dihedral : 4.548 18.974 808 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.51 % Allowed : 21.97 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.18 (0.34), residues: 654 helix: 2.68 (0.51), residues: 100 sheet: 0.61 (0.33), residues: 255 loop : -1.27 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.001 0.001 HIS H 38 PHE 0.029 0.002 PHE A 87 TYR 0.015 0.002 TYR L 92 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7532 (tp) REVERT: A 215 ASP cc_start: 0.7818 (t0) cc_final: 0.7604 (t0) REVERT: A 268 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6615 (mp0) REVERT: A 367 SER cc_start: 0.8772 (t) cc_final: 0.8173 (p) outliers start: 20 outliers final: 16 residues processed: 129 average time/residue: 0.2203 time to fit residues: 35.5445 Evaluate side-chains 133 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 22 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111148 restraints weight = 7989.872| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.66 r_work: 0.3205 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5350 Z= 0.229 Angle : 0.580 5.927 7273 Z= 0.300 Chirality : 0.043 0.162 825 Planarity : 0.005 0.052 927 Dihedral : 4.492 18.928 808 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.39 % Allowed : 21.09 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.23 (0.34), residues: 654 helix: 2.75 (0.52), residues: 100 sheet: 0.65 (0.33), residues: 255 loop : -1.25 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.001 0.001 HIS A 30 PHE 0.030 0.002 PHE A 87 TYR 0.014 0.001 TYR L 92 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7537 (tp) REVERT: A 59 CYS cc_start: 0.7261 (OUTLIER) cc_final: 0.7020 (t) REVERT: A 215 ASP cc_start: 0.7819 (t0) cc_final: 0.7547 (t0) REVERT: A 268 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6582 (mp0) REVERT: A 296 LYS cc_start: 0.7806 (mttt) cc_final: 0.7591 (mmmm) REVERT: A 349 GLN cc_start: 0.7399 (tt0) cc_final: 0.7129 (tp40) REVERT: A 367 SER cc_start: 0.8783 (t) cc_final: 0.8179 (p) outliers start: 25 outliers final: 18 residues processed: 133 average time/residue: 0.2197 time to fit residues: 36.2332 Evaluate side-chains 137 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 5 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110038 restraints weight = 7983.721| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.67 r_work: 0.3193 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5350 Z= 0.243 Angle : 0.587 6.026 7273 Z= 0.304 Chirality : 0.043 0.167 825 Planarity : 0.005 0.050 927 Dihedral : 4.485 18.897 808 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.04 % Allowed : 21.62 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.23 (0.34), residues: 654 helix: 2.74 (0.52), residues: 100 sheet: 0.68 (0.33), residues: 255 loop : -1.26 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.002 0.001 HIS A 30 PHE 0.031 0.002 PHE A 87 TYR 0.015 0.001 TYR L 92 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7079 (t) REVERT: A 134 GLU cc_start: 0.6807 (mp0) cc_final: 0.6322 (mp0) REVERT: A 215 ASP cc_start: 0.7870 (t0) cc_final: 0.7554 (t0) REVERT: A 268 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6559 (mp0) REVERT: A 296 LYS cc_start: 0.7784 (mttt) cc_final: 0.7578 (mmmm) REVERT: A 367 SER cc_start: 0.8775 (t) cc_final: 0.8167 (p) outliers start: 23 outliers final: 18 residues processed: 133 average time/residue: 0.2086 time to fit residues: 34.1544 Evaluate side-chains 136 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 38 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.0570 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110942 restraints weight = 8037.487| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.51 r_work: 0.3199 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5350 Z= 0.279 Angle : 0.616 9.574 7273 Z= 0.317 Chirality : 0.044 0.178 825 Planarity : 0.005 0.050 927 Dihedral : 4.604 19.156 808 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.69 % Allowed : 22.32 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.22 (0.34), residues: 654 helix: 2.70 (0.52), residues: 100 sheet: 0.75 (0.34), residues: 253 loop : -1.33 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 111 HIS 0.002 0.001 HIS A 320 PHE 0.032 0.002 PHE A 87 TYR 0.016 0.002 TYR L 92 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8251 (tttp) REVERT: A 133 PRO cc_start: 0.7732 (Cg_endo) cc_final: 0.6973 (Cg_exo) REVERT: A 134 GLU cc_start: 0.6816 (mp0) cc_final: 0.5975 (mp0) REVERT: A 215 ASP cc_start: 0.8053 (t0) cc_final: 0.7762 (t0) REVERT: A 268 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6771 (mp0) REVERT: A 296 LYS cc_start: 0.7833 (mttt) cc_final: 0.7615 (mmmm) REVERT: A 330 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7835 (tppt) REVERT: A 367 SER cc_start: 0.8818 (t) cc_final: 0.8208 (p) outliers start: 21 outliers final: 17 residues processed: 133 average time/residue: 0.2193 time to fit residues: 35.9873 Evaluate side-chains 137 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110370 restraints weight = 8006.327| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.68 r_work: 0.3182 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5350 Z= 0.264 Angle : 0.609 9.205 7273 Z= 0.313 Chirality : 0.044 0.176 825 Planarity : 0.005 0.050 927 Dihedral : 4.596 19.190 808 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.34 % Allowed : 22.14 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.23 (0.34), residues: 654 helix: 2.73 (0.52), residues: 100 sheet: 0.74 (0.34), residues: 255 loop : -1.33 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.002 0.001 HIS A 30 PHE 0.031 0.002 PHE A 87 TYR 0.015 0.002 TYR L 92 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8132 (tttp) REVERT: A 133 PRO cc_start: 0.7735 (Cg_endo) cc_final: 0.6974 (Cg_exo) REVERT: A 134 GLU cc_start: 0.6860 (mp0) cc_final: 0.6190 (mp0) REVERT: A 215 ASP cc_start: 0.7932 (t0) cc_final: 0.7616 (t0) REVERT: A 268 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6579 (mp0) REVERT: A 330 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7690 (tppt) REVERT: A 367 SER cc_start: 0.8778 (t) cc_final: 0.8155 (p) outliers start: 19 outliers final: 18 residues processed: 130 average time/residue: 0.2146 time to fit residues: 34.3968 Evaluate side-chains 137 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.0040 chunk 40 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 overall best weight: 0.2970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110219 restraints weight = 8028.533| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.63 r_work: 0.3212 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5350 Z= 0.208 Angle : 0.576 6.372 7273 Z= 0.298 Chirality : 0.043 0.156 825 Planarity : 0.005 0.050 927 Dihedral : 4.405 19.110 808 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.99 % Allowed : 22.50 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.32 (0.34), residues: 654 helix: 2.81 (0.52), residues: 100 sheet: 0.84 (0.34), residues: 253 loop : -1.30 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.002 0.001 HIS A 30 PHE 0.031 0.002 PHE A 87 TYR 0.012 0.001 TYR L 92 ARG 0.002 0.000 ARG A 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 GLU cc_start: 0.8166 (tt0) cc_final: 0.7936 (tt0) REVERT: A 10 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8139 (tttp) REVERT: A 133 PRO cc_start: 0.7735 (Cg_endo) cc_final: 0.7112 (Cg_exo) REVERT: A 134 GLU cc_start: 0.6859 (mp0) cc_final: 0.6224 (mp0) REVERT: A 215 ASP cc_start: 0.7892 (t0) cc_final: 0.7668 (t0) REVERT: A 268 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6573 (mp0) REVERT: A 330 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7690 (tppt) outliers start: 17 outliers final: 15 residues processed: 131 average time/residue: 0.2183 time to fit residues: 35.1444 Evaluate side-chains 133 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 15 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108790 restraints weight = 8105.751| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.63 r_work: 0.3185 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5350 Z= 0.286 Angle : 0.611 6.285 7273 Z= 0.318 Chirality : 0.044 0.178 825 Planarity : 0.005 0.051 927 Dihedral : 4.570 19.559 808 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.99 % Allowed : 23.02 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.23 (0.34), residues: 654 helix: 2.70 (0.52), residues: 100 sheet: 0.77 (0.34), residues: 255 loop : -1.35 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 111 HIS 0.002 0.001 HIS A 30 PHE 0.031 0.002 PHE A 87 TYR 0.017 0.002 TYR L 92 ARG 0.003 0.000 ARG A 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.92 seconds wall clock time: 47 minutes 42.58 seconds (2862.58 seconds total)