Starting phenix.real_space_refine on Wed Sep 17 05:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dnm_47042/09_2025/9dnm_47042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dnm_47042/09_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_47042/09_2025/9dnm_47042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dnm_47042/09_2025/9dnm_47042.map" model { file = "/net/cci-nas-00/data/ceres_data/9dnm_47042/09_2025/9dnm_47042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dnm_47042/09_2025/9dnm_47042.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU: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: 1.63, per 1000 atoms: 0.31 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: 0.50 Conformation dependent library (CDL) restraints added in 213.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.21 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: 0.84 Time building geometry restraints manager: 0.62 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.380 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.150 ------------------------------------------------------------------------------- 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 5352 Z= 0.196 Angle : 0.627 7.013 7277 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 76 TYR 0.016 0.001 TYR L 92 PHE 0.016 0.002 PHE A 450 TRP 0.008 0.001 TRP H 39 HIS 0.001 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 5350) covalent geometry : angle 0.62672 ( 7273) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.39975 ( 4) hydrogen bonds : bond 0.22003 ( 206) hydrogen bonds : angle 7.93911 ( 564) *********************** 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 : 0.206 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: 0.1112 time to fit residues: 17.1435 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 : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.127689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107993 restraints weight = 7972.483| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.73 r_work: 0.3179 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5352 Z= 0.238 Angle : 0.664 7.701 7277 Z= 0.346 Chirality : 0.046 0.201 825 Planarity : 0.006 0.073 927 Dihedral : 5.271 19.946 808 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.39 % Allowed : 19.33 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.33), residues: 654 helix: 2.47 (0.52), residues: 99 sheet: 0.02 (0.33), residues: 247 loop : -1.30 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 165 TYR 0.021 0.002 TYR H 53 PHE 0.020 0.002 PHE A 117 TRP 0.012 0.002 TRP H 111 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 5350) covalent geometry : angle 0.66414 ( 7273) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.84925 ( 4) hydrogen bonds : bond 0.05461 ( 206) hydrogen bonds : angle 5.59710 ( 564) *********************** 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 150 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8445 (ttp-170) cc_final: 0.7723 (ttt180) REVERT: L 10 SER cc_start: 0.8319 (m) cc_final: 0.8014 (t) REVERT: A 57 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7493 (tp) REVERT: A 268 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6732 (mp0) REVERT: A 367 SER cc_start: 0.8744 (t) cc_final: 0.8169 (p) REVERT: A 386 ARG cc_start: 0.7181 (ttm110) cc_final: 0.6277 (ttm110) outliers start: 25 outliers final: 14 residues processed: 141 average time/residue: 0.1007 time to fit residues: 17.5492 Evaluate side-chains 136 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 3 ILE 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 A residue 10 LYS 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 166 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.128169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108638 restraints weight = 7906.351| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.71 r_work: 0.3174 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5352 Z= 0.176 Angle : 0.610 6.697 7277 Z= 0.319 Chirality : 0.044 0.189 825 Planarity : 0.005 0.063 927 Dihedral : 4.835 19.255 808 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.99 % Allowed : 22.14 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.33), residues: 654 helix: 2.51 (0.52), residues: 99 sheet: 0.25 (0.33), residues: 252 loop : -1.29 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.017 0.002 TYR H 53 PHE 0.016 0.002 PHE A 450 TRP 0.010 0.001 TRP H 111 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5350) covalent geometry : angle 0.61014 ( 7273) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.62947 ( 4) hydrogen bonds : bond 0.04647 ( 206) hydrogen bonds : angle 5.21970 ( 564) *********************** 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 144 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.7767 (ttt180) REVERT: L 10 SER cc_start: 0.8325 (m) cc_final: 0.8012 (t) REVERT: A 268 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6622 (mp0) REVERT: A 274 ARG cc_start: 0.8269 (tpt170) cc_final: 0.7783 (tpp-160) REVERT: A 330 LYS cc_start: 0.7783 (tppt) cc_final: 0.7544 (tptp) REVERT: A 367 SER cc_start: 0.8730 (t) cc_final: 0.8125 (p) outliers start: 17 outliers final: 16 residues processed: 138 average time/residue: 0.1030 time to fit residues: 17.4328 Evaluate side-chains 144 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL 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 91 GLN 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 108 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 291 PHE 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 430 VAL 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 51 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.0470 chunk 3 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.128408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109672 restraints weight = 7922.231| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.65 r_work: 0.3180 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5352 Z= 0.172 Angle : 0.598 6.296 7277 Z= 0.312 Chirality : 0.043 0.178 825 Planarity : 0.005 0.059 927 Dihedral : 4.717 18.893 808 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.16 % Allowed : 22.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.34), residues: 654 helix: 2.65 (0.52), residues: 99 sheet: 0.40 (0.33), residues: 252 loop : -1.30 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.016 0.002 TYR L 92 PHE 0.016 0.002 PHE A 450 TRP 0.009 0.002 TRP H 111 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5350) covalent geometry : angle 0.59795 ( 7273) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.03903 ( 4) hydrogen bonds : bond 0.04419 ( 206) hydrogen bonds : angle 5.02409 ( 564) *********************** 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 140 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8428 (ttp-170) cc_final: 0.7754 (ttt180) REVERT: L 10 SER cc_start: 0.8332 (m) cc_final: 0.7996 (t) REVERT: A 134 GLU cc_start: 0.6489 (mp0) cc_final: 0.5855 (mp0) REVERT: A 215 ASP cc_start: 0.7773 (t0) cc_final: 0.7568 (t0) REVERT: A 268 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6590 (mp0) REVERT: A 367 SER cc_start: 0.8727 (t) cc_final: 0.8126 (p) outliers start: 18 outliers final: 16 residues processed: 132 average time/residue: 0.1007 time to fit residues: 16.4584 Evaluate side-chains 135 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 83 ASP 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 62 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 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 346 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 = 0.3573 r_free = 0.3573 target = 0.126382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108380 restraints weight = 8195.518| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.48 r_work: 0.3175 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5352 Z= 0.253 Angle : 0.656 7.438 7277 Z= 0.344 Chirality : 0.045 0.207 825 Planarity : 0.005 0.058 927 Dihedral : 4.981 19.139 808 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.69 % Allowed : 23.55 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.33), residues: 654 helix: 2.47 (0.50), residues: 99 sheet: 0.27 (0.33), residues: 252 loop : -1.44 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.020 0.002 TYR L 92 PHE 0.019 0.002 PHE A 450 TRP 0.011 0.002 TRP H 111 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 5350) covalent geometry : angle 0.65558 ( 7273) SS BOND : bond 0.00124 ( 2) SS BOND : angle 1.20224 ( 4) hydrogen bonds : bond 0.04987 ( 206) hydrogen bonds : angle 5.14432 ( 564) *********************** 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 143 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8521 (ttp-170) cc_final: 0.7856 (ttt180) REVERT: L 10 SER cc_start: 0.8385 (m) cc_final: 0.8052 (t) REVERT: A 215 ASP cc_start: 0.8010 (t0) cc_final: 0.7796 (t0) REVERT: A 268 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6793 (mp0) REVERT: A 341 ASP cc_start: 0.7999 (p0) cc_final: 0.7619 (p0) REVERT: A 367 SER cc_start: 0.8794 (t) cc_final: 0.8211 (p) outliers start: 21 outliers final: 17 residues processed: 134 average time/residue: 0.0973 time to fit residues: 16.1908 Evaluate side-chains 135 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL 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 89 CYS 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 172 GLN Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 430 VAL 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 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 48 optimal weight: 0.0370 chunk 37 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.128911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110290 restraints weight = 8075.405| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.63 r_work: 0.3202 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5352 Z= 0.135 Angle : 0.581 5.917 7277 Z= 0.304 Chirality : 0.043 0.163 825 Planarity : 0.005 0.054 927 Dihedral : 4.508 18.676 808 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.51 % Allowed : 23.55 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.34), residues: 654 helix: 2.69 (0.51), residues: 99 sheet: 0.52 (0.34), residues: 252 loop : -1.30 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.011 0.001 TYR L 92 PHE 0.015 0.002 PHE A 450 TRP 0.009 0.001 TRP H 111 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5350) covalent geometry : angle 0.58023 ( 7273) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.95948 ( 4) hydrogen bonds : bond 0.03905 ( 206) hydrogen bonds : angle 4.79981 ( 564) *********************** 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 141 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7762 (ttt180) REVERT: L 10 SER cc_start: 0.8354 (m) cc_final: 0.7876 (p) REVERT: A 15 ASN cc_start: 0.6547 (m-40) cc_final: 0.6197 (m110) REVERT: A 38 ASP cc_start: 0.7008 (p0) cc_final: 0.6789 (p0) REVERT: A 57 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7539 (tp) REVERT: A 215 ASP cc_start: 0.7800 (t0) cc_final: 0.7500 (t0) REVERT: A 268 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6598 (mp0) REVERT: A 341 ASP cc_start: 0.7804 (p0) cc_final: 0.7468 (p0) REVERT: A 367 SER cc_start: 0.8760 (t) cc_final: 0.8171 (p) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.1017 time to fit residues: 16.5204 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL 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 172 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 346 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 = 0.3586 r_free = 0.3586 target = 0.127621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108824 restraints weight = 8090.001| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.67 r_work: 0.3171 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5352 Z= 0.216 Angle : 0.635 6.795 7277 Z= 0.332 Chirality : 0.044 0.191 825 Planarity : 0.005 0.054 927 Dihedral : 4.739 18.950 808 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.87 % Allowed : 23.02 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.33), residues: 654 helix: 2.51 (0.50), residues: 99 sheet: 0.46 (0.33), residues: 258 loop : -1.48 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.018 0.002 TYR L 92 PHE 0.017 0.002 PHE A 450 TRP 0.010 0.002 TRP H 111 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 5350) covalent geometry : angle 0.63461 ( 7273) SS BOND : bond 0.00217 ( 2) SS BOND : angle 1.08814 ( 4) hydrogen bonds : bond 0.04562 ( 206) hydrogen bonds : angle 4.89108 ( 564) *********************** 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 143 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.7782 (ttt180) REVERT: L 10 SER cc_start: 0.8368 (m) cc_final: 0.7882 (p) REVERT: A 38 ASP cc_start: 0.7085 (p0) cc_final: 0.6853 (p0) REVERT: A 133 PRO cc_start: 0.7784 (Cg_exo) cc_final: 0.7554 (Cg_endo) REVERT: A 215 ASP cc_start: 0.7925 (t0) cc_final: 0.7616 (t0) REVERT: A 268 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6578 (mp0) REVERT: A 330 LYS cc_start: 0.7781 (tppt) cc_final: 0.7460 (tppt) REVERT: A 341 ASP cc_start: 0.7796 (p0) cc_final: 0.7424 (p0) REVERT: A 367 SER cc_start: 0.8772 (t) cc_final: 0.8164 (p) outliers start: 22 outliers final: 19 residues processed: 135 average time/residue: 0.0985 time to fit residues: 16.4873 Evaluate side-chains 140 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL 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 172 GLN Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 286 GLU 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 430 VAL 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 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.0270 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 346 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 = 0.3593 r_free = 0.3593 target = 0.127993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109311 restraints weight = 7999.065| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.65 r_work: 0.3183 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5352 Z= 0.179 Angle : 0.617 6.344 7277 Z= 0.321 Chirality : 0.043 0.179 825 Planarity : 0.005 0.053 927 Dihedral : 4.692 18.857 808 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.51 % Allowed : 23.37 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.34), residues: 654 helix: 2.55 (0.50), residues: 99 sheet: 0.54 (0.34), residues: 258 loop : -1.49 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.016 0.002 TYR L 92 PHE 0.017 0.002 PHE A 450 TRP 0.009 0.002 TRP H 111 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 5350) covalent geometry : angle 0.61641 ( 7273) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.01896 ( 4) hydrogen bonds : bond 0.04301 ( 206) hydrogen bonds : angle 4.83951 ( 564) *********************** 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 137 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8437 (ttp-170) cc_final: 0.7779 (ttt180) REVERT: L 10 SER cc_start: 0.8368 (m) cc_final: 0.7888 (p) REVERT: A 38 ASP cc_start: 0.7064 (p0) cc_final: 0.6810 (p0) REVERT: A 57 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7484 (tp) REVERT: A 122 ASN cc_start: 0.7103 (t0) cc_final: 0.6858 (t0) REVERT: A 133 PRO cc_start: 0.7634 (Cg_exo) cc_final: 0.7152 (Cg_endo) REVERT: A 134 GLU cc_start: 0.6722 (mp0) cc_final: 0.6280 (mp0) REVERT: A 215 ASP cc_start: 0.7908 (t0) cc_final: 0.7576 (t0) REVERT: A 268 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6594 (mp0) REVERT: A 330 LYS cc_start: 0.7779 (tppt) cc_final: 0.7362 (tppt) REVERT: A 341 ASP cc_start: 0.7773 (p0) cc_final: 0.7399 (p0) REVERT: A 367 SER cc_start: 0.8766 (t) cc_final: 0.8155 (p) outliers start: 20 outliers final: 17 residues processed: 130 average time/residue: 0.0993 time to fit residues: 15.8416 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 : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL 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 172 GLN Chi-restraints excluded: chain A residue 286 GLU 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 430 VAL 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 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 346 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 = 0.3586 r_free = 0.3586 target = 0.127505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108769 restraints weight = 8083.021| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.67 r_work: 0.3171 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5352 Z= 0.215 Angle : 0.636 6.835 7277 Z= 0.331 Chirality : 0.044 0.192 825 Planarity : 0.005 0.055 927 Dihedral : 4.784 19.086 808 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.51 % Allowed : 23.37 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.33), residues: 654 helix: 2.51 (0.50), residues: 99 sheet: 0.51 (0.34), residues: 258 loop : -1.55 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.019 0.002 TYR H 53 PHE 0.018 0.002 PHE A 450 TRP 0.010 0.002 TRP H 111 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 5350) covalent geometry : angle 0.63548 ( 7273) SS BOND : bond 0.00239 ( 2) SS BOND : angle 1.09860 ( 4) hydrogen bonds : bond 0.04538 ( 206) hydrogen bonds : angle 4.88036 ( 564) *********************** 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 142 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.7787 (ttt180) REVERT: L 10 SER cc_start: 0.8372 (m) cc_final: 0.7890 (p) REVERT: A 38 ASP cc_start: 0.7100 (p0) cc_final: 0.6853 (p0) REVERT: A 133 PRO cc_start: 0.7676 (Cg_exo) cc_final: 0.7424 (Cg_endo) REVERT: A 134 GLU cc_start: 0.6781 (mp0) cc_final: 0.6287 (mp0) REVERT: A 215 ASP cc_start: 0.7943 (t0) cc_final: 0.7623 (t0) REVERT: A 268 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6590 (mp0) REVERT: A 341 ASP cc_start: 0.7769 (p0) cc_final: 0.7386 (p0) REVERT: A 367 SER cc_start: 0.8776 (t) cc_final: 0.8171 (p) outliers start: 20 outliers final: 19 residues processed: 135 average time/residue: 0.0988 time to fit residues: 16.6017 Evaluate side-chains 140 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 124 THR 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 172 GLN Chi-restraints excluded: chain A residue 286 GLU 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 430 VAL 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 62 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.0020 chunk 51 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 57 optimal weight: 0.5980 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 346 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 = 0.128350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110401 restraints weight = 8040.706| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.47 r_work: 0.3210 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5352 Z= 0.157 Angle : 0.617 6.949 7277 Z= 0.322 Chirality : 0.043 0.170 825 Planarity : 0.005 0.052 927 Dihedral : 4.616 19.131 808 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.99 % Allowed : 24.43 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.34), residues: 654 helix: 2.67 (0.51), residues: 99 sheet: 0.61 (0.34), residues: 258 loop : -1.48 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.014 0.001 TYR L 92 PHE 0.017 0.002 PHE A 450 TRP 0.010 0.001 TRP H 111 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 5350) covalent geometry : angle 0.61705 ( 7273) SS BOND : bond 0.00372 ( 2) SS BOND : angle 1.02736 ( 4) hydrogen bonds : bond 0.04093 ( 206) hydrogen bonds : angle 4.77171 ( 564) ********************** 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 135 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: H 101 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.7839 (ttt180) REVERT: L 10 SER cc_start: 0.8384 (m) cc_final: 0.7930 (p) REVERT: A 38 ASP cc_start: 0.7193 (p0) cc_final: 0.6956 (p0) REVERT: A 57 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7596 (tp) REVERT: A 133 PRO cc_start: 0.7697 (Cg_exo) cc_final: 0.7419 (Cg_endo) REVERT: A 134 GLU cc_start: 0.6785 (mp0) cc_final: 0.6295 (mp0) REVERT: A 215 ASP cc_start: 0.8030 (t0) cc_final: 0.7826 (t0) REVERT: A 268 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6765 (mp0) REVERT: A 330 LYS cc_start: 0.7897 (tppt) cc_final: 0.7637 (tppt) REVERT: A 341 ASP cc_start: 0.7969 (p0) cc_final: 0.7605 (p0) REVERT: A 367 SER cc_start: 0.8797 (t) cc_final: 0.8184 (p) outliers start: 17 outliers final: 16 residues processed: 128 average time/residue: 0.0968 time to fit residues: 15.3274 Evaluate side-chains 135 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL 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 172 GLN Chi-restraints excluded: chain A residue 286 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 13 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 overall best weight: 0.2398 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.129813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111649 restraints weight = 8105.495| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.51 r_work: 0.3223 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5352 Z= 0.130 Angle : 0.589 6.633 7277 Z= 0.307 Chirality : 0.042 0.152 825 Planarity : 0.005 0.051 927 Dihedral : 4.417 19.082 808 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.81 % Allowed : 24.60 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.34), residues: 654 helix: 2.75 (0.51), residues: 100 sheet: 0.71 (0.34), residues: 258 loop : -1.42 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.012 0.001 TYR L 92 PHE 0.015 0.002 PHE A 450 TRP 0.009 0.001 TRP H 111 HIS 0.001 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5350) covalent geometry : angle 0.58889 ( 7273) SS BOND : bond 0.00340 ( 2) SS BOND : angle 0.68266 ( 4) hydrogen bonds : bond 0.03721 ( 206) hydrogen bonds : angle 4.65764 ( 564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.34 seconds wall clock time: 25 minutes 35.04 seconds (1535.04 seconds total)