Starting phenix.real_space_refine on Tue Feb 11 10:16:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dnm_47042/02_2025/9dnm_47042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dnm_47042/02_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_47042/02_2025/9dnm_47042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dnm_47042/02_2025/9dnm_47042.map" model { file = "/net/cci-nas-00/data/ceres_data/9dnm_47042/02_2025/9dnm_47042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dnm_47042/02_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-5592/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: 1.24 Conformation dependent library (CDL) restraints added in 619.0 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: 0.72 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: 1.55 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: 1.150 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.570 Find NCS groups from input model: 0.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- 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 : 0.561 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: 0.2357 time to fit residues: 36.3113 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 : 0.535 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111225 restraints weight = 7821.934| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.71 r_work: 0.3217 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- 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 : 0.545 Fit side-chains revert: symmetry clash REVERT: L 10 SER cc_start: 0.8259 (m) cc_final: 0.7965 (t) REVERT: A 57 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7445 (tp) REVERT: A 77 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7977 (mtmm) REVERT: A 227 LYS cc_start: 0.6875 (mppt) cc_final: 0.6643 (mppt) REVERT: A 268 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6735 (mp0) REVERT: A 301 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6779 (tt0) REVERT: A 367 SER cc_start: 0.8734 (t) cc_final: 0.8156 (p) REVERT: A 386 ARG cc_start: 0.7088 (ttm110) cc_final: 0.6187 (ttm110) outliers start: 20 outliers final: 8 residues processed: 135 average time/residue: 0.2358 time to fit residues: 38.7442 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 : 0.601 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.3581 r_free = 0.3581 target = 0.126890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108069 restraints weight = 8006.690| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.65 r_work: 0.3167 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 5350 Z= 0.378 Angle : 0.659 7.383 7273 Z= 0.345 Chirality : 0.045 0.205 825 Planarity : 0.006 0.062 927 Dihedral : 4.998 19.783 808 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.39 % Allowed : 19.68 % 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: -0.07 (0.33), residues: 654 helix: 2.58 (0.52), residues: 99 sheet: 0.33 (0.33), residues: 255 loop : -1.33 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 111 HIS 0.003 0.001 HIS H 38 PHE 0.028 0.002 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 152 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 94 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8730 (p) REVERT: H 101 ARG cc_start: 0.8445 (ttp-170) cc_final: 0.7766 (ttt180) REVERT: L 10 SER cc_start: 0.8328 (m) cc_final: 0.8001 (t) REVERT: A 59 CYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7135 (t) REVERT: A 268 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6636 (mp0) REVERT: A 274 ARG cc_start: 0.8291 (tpt170) cc_final: 0.7767 (tpp-160) REVERT: A 330 LYS cc_start: 0.7794 (tppt) cc_final: 0.7553 (tptp) REVERT: A 367 SER cc_start: 0.8755 (t) cc_final: 0.8181 (p) outliers start: 25 outliers final: 18 residues processed: 140 average time/residue: 0.2146 time to fit residues: 37.4122 Evaluate side-chains 145 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 291 PHE 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: 0.5980 chunk 22 optimal weight: 0.0370 chunk 25 optimal weight: 0.0570 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 11 optimal weight: 0.0870 chunk 40 optimal weight: 0.6980 overall best weight: 0.1512 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.130705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111380 restraints weight = 8093.590| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.67 r_work: 0.3220 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5350 Z= 0.155 Angle : 0.549 5.823 7273 Z= 0.287 Chirality : 0.042 0.140 825 Planarity : 0.005 0.057 927 Dihedral : 4.386 18.992 808 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.28 % Allowed : 22.32 % Favored : 75.40 % 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: 0.25 (0.34), residues: 654 helix: 2.77 (0.52), residues: 100 sheet: 0.58 (0.33), residues: 255 loop : -1.15 (0.36), 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 L 88 ARG 0.002 0.000 ARG H 41 *********************** 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 128 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 10 SER cc_start: 0.8313 (m) cc_final: 0.8002 (t) REVERT: A 57 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7532 (tp) REVERT: A 268 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6633 (mp0) REVERT: A 367 SER cc_start: 0.8752 (t) cc_final: 0.8157 (p) outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 0.2308 time to fit residues: 35.2846 Evaluate side-chains 120 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 291 PHE Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.129525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110694 restraints weight = 7984.850| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.67 r_work: 0.3198 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1397 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= 0.267 Angle : 0.590 6.048 7273 Z= 0.308 Chirality : 0.043 0.169 825 Planarity : 0.005 0.054 927 Dihedral : 4.537 19.029 808 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.16 % Allowed : 22.50 % 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: 0.19 (0.34), residues: 654 helix: 2.71 (0.51), residues: 100 sheet: 0.60 (0.33), residues: 255 loop : -1.24 (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 H 38 PHE 0.028 0.002 PHE A 87 TYR 0.016 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: 18 poor density : 119 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 10 SER cc_start: 0.8333 (m) cc_final: 0.8008 (t) REVERT: A 38 ASP cc_start: 0.7138 (p0) cc_final: 0.6864 (p0) REVERT: A 215 ASP cc_start: 0.7811 (t0) cc_final: 0.7581 (t0) REVERT: A 268 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6603 (mp0) REVERT: A 274 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7734 (tpp-160) REVERT: A 367 SER cc_start: 0.8770 (t) cc_final: 0.8171 (p) outliers start: 18 outliers final: 17 residues processed: 131 average time/residue: 0.2565 time to fit residues: 41.4143 Evaluate side-chains 136 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 91 GLN 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 108 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.0070 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108397 restraints weight = 8013.446| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.65 r_work: 0.3177 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5350 Z= 0.308 Angle : 0.619 6.682 7273 Z= 0.323 Chirality : 0.044 0.190 825 Planarity : 0.005 0.053 927 Dihedral : 4.727 19.243 808 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.04 % Allowed : 21.97 % 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: 0.12 (0.33), residues: 654 helix: 2.66 (0.52), residues: 100 sheet: 0.60 (0.33), residues: 255 loop : -1.34 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 111 HIS 0.002 0.001 HIS H 38 PHE 0.029 0.002 PHE A 87 TYR 0.018 0.002 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 145 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 14 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7736 (mt) REVERT: L 10 SER cc_start: 0.8355 (m) cc_final: 0.8011 (t) REVERT: A 38 ASP cc_start: 0.7205 (p0) cc_final: 0.6922 (p0) REVERT: A 59 CYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7070 (t) REVERT: A 133 PRO cc_start: 0.7680 (Cg_endo) cc_final: 0.7305 (Cg_exo) REVERT: A 134 GLU cc_start: 0.6757 (mp0) cc_final: 0.6223 (mp0) REVERT: A 215 ASP cc_start: 0.7919 (t0) cc_final: 0.7600 (t0) REVERT: A 268 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6602 (mp0) REVERT: A 296 LYS cc_start: 0.7797 (mttt) cc_final: 0.7583 (mmmm) REVERT: A 317 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8176 (m) REVERT: A 367 SER cc_start: 0.8774 (t) cc_final: 0.8183 (p) outliers start: 23 outliers final: 15 residues processed: 138 average time/residue: 0.2109 time to fit residues: 36.1194 Evaluate side-chains 139 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 14 LEU 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 A residue 10 LYS 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 271 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 317 VAL 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: 0.1980 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.128807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110160 restraints weight = 7966.551| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.66 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: 0.7419 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5350 Z= 0.266 Angle : 0.601 6.421 7273 Z= 0.312 Chirality : 0.044 0.181 825 Planarity : 0.005 0.053 927 Dihedral : 4.622 18.994 808 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.69 % Allowed : 21.97 % 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: 0.16 (0.34), residues: 654 helix: 2.74 (0.52), residues: 100 sheet: 0.64 (0.33), residues: 255 loop : -1.34 (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 0.015 0.002 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 142 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 14 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7753 (mt) REVERT: L 10 SER cc_start: 0.8358 (m) cc_final: 0.7880 (p) REVERT: A 38 ASP cc_start: 0.7160 (p0) cc_final: 0.6891 (p0) REVERT: A 57 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7499 (tp) REVERT: A 133 PRO cc_start: 0.7677 (Cg_endo) cc_final: 0.7299 (Cg_exo) REVERT: A 134 GLU cc_start: 0.6756 (mp0) cc_final: 0.6174 (mp0) REVERT: A 215 ASP cc_start: 0.7915 (t0) cc_final: 0.7604 (t0) REVERT: A 268 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6572 (mp0) REVERT: A 296 LYS cc_start: 0.7783 (mttt) cc_final: 0.7567 (mmmm) REVERT: A 330 LYS cc_start: 0.7766 (tppt) cc_final: 0.7353 (tppt) REVERT: A 367 SER cc_start: 0.8764 (t) cc_final: 0.8155 (p) outliers start: 21 outliers final: 17 residues processed: 136 average time/residue: 0.2124 time to fit residues: 35.5097 Evaluate side-chains 139 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 14 LEU 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 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 186 LEU Chi-restraints excluded: chain A residue 254 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 10 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 0.0770 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 overall best weight: 0.2536 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.129290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111368 restraints weight = 8048.461| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.48 r_work: 0.3228 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5350 Z= 0.189 Angle : 0.559 5.740 7273 Z= 0.289 Chirality : 0.042 0.150 825 Planarity : 0.005 0.051 927 Dihedral : 4.344 19.004 808 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.16 % Allowed : 22.50 % 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: 0.34 (0.34), residues: 654 helix: 2.87 (0.52), residues: 100 sheet: 0.85 (0.34), residues: 253 loop : -1.31 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 111 HIS 0.002 0.001 HIS A 320 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 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 135 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 14 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7772 (mt) REVERT: H 49 GLU cc_start: 0.8307 (tt0) cc_final: 0.8085 (tt0) REVERT: L 10 SER cc_start: 0.8382 (m) cc_final: 0.7939 (p) REVERT: A 38 ASP cc_start: 0.7270 (p0) cc_final: 0.6984 (p0) REVERT: A 133 PRO cc_start: 0.7666 (Cg_endo) cc_final: 0.7010 (Cg_exo) REVERT: A 134 GLU cc_start: 0.6728 (mp0) cc_final: 0.6044 (mp0) REVERT: A 215 ASP cc_start: 0.7992 (t0) cc_final: 0.7779 (t0) REVERT: A 268 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6811 (mp0) REVERT: A 341 ASP cc_start: 0.7969 (p0) cc_final: 0.7625 (p0) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 0.2180 time to fit residues: 34.6121 Evaluate side-chains 129 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 14 LEU 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 56 THR Chi-restraints excluded: chain A residue 108 LEU 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 298 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: 0.9990 chunk 64 optimal weight: 0.1980 chunk 29 optimal weight: 0.0070 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.0050 chunk 5 optimal weight: 0.0050 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.1426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112471 restraints weight = 8045.318| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.61 r_work: 0.3237 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5350 Z= 0.156 Angle : 0.545 6.635 7273 Z= 0.280 Chirality : 0.042 0.151 825 Planarity : 0.005 0.050 927 Dihedral : 4.071 18.615 808 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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: 0.49 (0.34), residues: 654 helix: 2.85 (0.52), residues: 100 sheet: 0.97 (0.34), residues: 253 loop : -1.20 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.001 0.000 HIS A 299 PHE 0.031 0.002 PHE A 87 TYR 0.009 0.001 TYR L 92 ARG 0.002 0.000 ARG A 76 *********************** 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 134 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 14 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7687 (mt) REVERT: L 10 SER cc_start: 0.8347 (m) cc_final: 0.7912 (p) REVERT: A 38 ASP cc_start: 0.7040 (p0) cc_final: 0.6786 (p0) REVERT: A 133 PRO cc_start: 0.7662 (Cg_endo) cc_final: 0.7017 (Cg_exo) REVERT: A 134 GLU cc_start: 0.6749 (mp0) cc_final: 0.6045 (mp0) REVERT: A 268 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6563 (mp0) REVERT: A 330 LYS cc_start: 0.7734 (tppt) cc_final: 0.7393 (tppt) REVERT: A 341 ASP cc_start: 0.7793 (p0) cc_final: 0.7440 (p0) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 0.2070 time to fit residues: 32.9339 Evaluate side-chains 127 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 14 LEU 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 104 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 298 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: 0.9980 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 37 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** 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 = 0.3590 r_free = 0.3590 target = 0.127621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109980 restraints weight = 8081.916| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.44 r_work: 0.3212 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5350 Z= 0.321 Angle : 0.633 6.354 7273 Z= 0.328 Chirality : 0.044 0.174 825 Planarity : 0.005 0.051 927 Dihedral : 4.526 19.094 808 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.64 % Allowed : 22.85 % 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: 0.35 (0.34), residues: 654 helix: 2.76 (0.52), residues: 100 sheet: 0.92 (0.34), residues: 253 loop : -1.33 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 111 HIS 0.002 0.001 HIS A 159 PHE 0.030 0.002 PHE A 87 TYR 0.018 0.002 TYR H 53 ARG 0.003 0.000 ARG A 337 ********************** 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 140 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 14 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7810 (mt) REVERT: H 94 THR cc_start: 0.9069 (t) cc_final: 0.8705 (p) REVERT: L 10 SER cc_start: 0.8379 (m) cc_final: 0.7947 (p) REVERT: A 38 ASP cc_start: 0.7316 (p0) cc_final: 0.7050 (p0) REVERT: A 133 PRO cc_start: 0.7746 (Cg_endo) cc_final: 0.7357 (Cg_exo) REVERT: A 134 GLU cc_start: 0.6786 (mp0) cc_final: 0.6177 (mp0) REVERT: A 215 ASP cc_start: 0.8062 (t0) cc_final: 0.7842 (t0) REVERT: A 268 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6795 (mp0) REVERT: A 330 LYS cc_start: 0.7921 (tppt) cc_final: 0.7597 (tppt) REVERT: A 341 ASP cc_start: 0.7956 (p0) cc_final: 0.7603 (p0) REVERT: A 367 SER cc_start: 0.8814 (t) cc_final: 0.8197 (p) outliers start: 15 outliers final: 14 residues processed: 136 average time/residue: 0.2103 time to fit residues: 35.2150 Evaluate side-chains 138 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 14 LEU 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 104 THR Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU 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 298 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 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.128375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108989 restraints weight = 8033.134| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.72 r_work: 0.3186 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1809 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= 0.258 Angle : 0.614 6.541 7273 Z= 0.318 Chirality : 0.044 0.172 825 Planarity : 0.005 0.050 927 Dihedral : 4.477 19.437 808 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.64 % Allowed : 23.37 % 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: 0.32 (0.34), residues: 654 helix: 2.78 (0.51), residues: 100 sheet: 0.88 (0.34), residues: 253 loop : -1.34 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS A 30 PHE 0.032 0.002 PHE A 87 TYR 0.015 0.002 TYR L 92 ARG 0.002 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2601.33 seconds wall clock time: 47 minutes 1.36 seconds (2821.36 seconds total)