Starting phenix.real_space_refine on Thu Jul 2 00:27:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jd3_61379/07_2026/9jd3_61379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jd3_61379/07_2026/9jd3_61379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jd3_61379/07_2026/9jd3_61379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jd3_61379/07_2026/9jd3_61379.map" model { file = "/net/cci-nas-00/data/ceres_data/9jd3_61379/07_2026/9jd3_61379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jd3_61379/07_2026/9jd3_61379_neut.cif" } resolution = 3.2 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= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 3057 2.51 5 N 655 2.21 5 O 751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4496 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4311 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 184 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'CLR': 1, 'D10': 2, 'D12': 3, 'HEX': 7, 'LNK': 1, 'NAG': 1, 'OCT': 4} Classifications: {'undetermined': 19, 'water': 7} Link IDs: {None: 24} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.34, per 1000 atoms: 0.30 Number of scatterers: 4496 At special positions: 0 Unit cell: (88.62, 67.52, 87.565, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 32 16.00 O 751 8.00 N 655 7.00 C 3057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " 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=1, symmetry=0 Links applied NAG-ASN " NAG A 720 " - " ASN A 190 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 188.4 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 77.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.659A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 4.075A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.311A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 removed outlier: 4.441A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 Processing helix chain 'A' and resid 245 through 267 removed outlier: 4.064A pdb=" N THR A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.646A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 removed outlier: 3.768A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 287' Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.274A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.646A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.031A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.645A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.576A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.536A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 448 through 449 No H-bonds generated for 'chain 'A' and resid 448 through 449' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.783A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.627A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.697A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 273 hydrogen bonds defined for protein. 807 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: 0.64 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1059 1.33 - 1.45: 993 1.45 - 1.57: 2517 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4615 Sorted by residual: bond pdb=" N GLU A 591 " pdb=" CA GLU A 591 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.15e-02 7.56e+03 8.53e+00 bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.59e+00 bond pdb=" N VAL A 590 " pdb=" CA VAL A 590 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.30e+00 bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.19e-02 7.06e+03 7.21e+00 bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.21e-02 6.83e+03 6.74e+00 ... (remaining 4610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 6039 1.55 - 3.09: 173 3.09 - 4.64: 24 4.64 - 6.19: 6 6.19 - 7.73: 4 Bond angle restraints: 6246 Sorted by residual: angle pdb=" CA ARG A 583 " pdb=" C ARG A 583 " pdb=" O ARG A 583 " ideal model delta sigma weight residual 122.41 117.96 4.45 1.21e+00 6.83e-01 1.35e+01 angle pdb=" N ARG A 587 " pdb=" CA ARG A 587 " pdb=" C ARG A 587 " ideal model delta sigma weight residual 113.16 108.65 4.51 1.24e+00 6.50e-01 1.32e+01 angle pdb=" N ALA A 589 " pdb=" CA ALA A 589 " pdb=" C ALA A 589 " ideal model delta sigma weight residual 113.61 108.32 5.29 1.50e+00 4.44e-01 1.24e+01 angle pdb=" CA SER A 205 " pdb=" C SER A 205 " pdb=" O SER A 205 " ideal model delta sigma weight residual 121.84 118.12 3.72 1.16e+00 7.43e-01 1.03e+01 angle pdb=" N SER A 205 " pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 111.39 106.98 4.41 1.38e+00 5.25e-01 1.02e+01 ... (remaining 6241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 2335 14.40 - 28.81: 256 28.81 - 43.21: 70 43.21 - 57.62: 15 57.62 - 72.02: 5 Dihedral angle restraints: 2681 sinusoidal: 1113 harmonic: 1568 Sorted by residual: dihedral pdb=" CB MET A 309 " pdb=" CG MET A 309 " pdb=" SD MET A 309 " pdb=" CE MET A 309 " ideal model delta sinusoidal sigma weight residual 180.00 125.73 54.27 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CB MET A 452 " pdb=" CG MET A 452 " pdb=" SD MET A 452 " pdb=" CE MET A 452 " ideal model delta sinusoidal sigma weight residual -180.00 -126.98 -53.02 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CA LYS A 115 " pdb=" CB LYS A 115 " pdb=" CG LYS A 115 " pdb=" CD LYS A 115 " ideal model delta sinusoidal sigma weight residual -180.00 -127.63 -52.37 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 2678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 684 0.310 - 0.620: 0 0.620 - 0.930: 0 0.930 - 1.240: 0 1.240 - 1.550: 1 Chirality restraints: 685 Sorted by residual: chirality pdb=" C1 NAG A 720 " pdb=" ND2 ASN A 190 " pdb=" C2 NAG A 720 " pdb=" O5 NAG A 720 " both_signs ideal model delta sigma weight residual False -2.40 -3.95 1.55 2.00e-01 2.50e+01 6.01e+01 chirality pdb=" CA ILE A 196 " pdb=" N ILE A 196 " pdb=" C ILE A 196 " pdb=" CB ILE A 196 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" C20 CLR A 718 " pdb=" C17 CLR A 718 " pdb=" C21 CLR A 718 " pdb=" C22 CLR A 718 " both_signs ideal model delta sigma weight residual False 2.59 2.41 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 682 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.050 2.00e-02 2.50e+03 6.22e-02 4.84e+01 pdb=" CG ASN A 190 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.087 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG A 720 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 720 " -0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG A 720 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 720 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 720 " 0.057 2.00e-02 2.50e+03 pdb=" O7 NAG A 720 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 583 " -0.258 9.50e-02 1.11e+02 1.16e-01 8.26e+00 pdb=" NE ARG A 583 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 583 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 583 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 583 " -0.008 2.00e-02 2.50e+03 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 1 1.84 - 2.61: 43 2.61 - 3.37: 6096 3.37 - 4.14: 10811 4.14 - 4.90: 21046 Nonbonded interactions: 37997 Sorted by model distance: nonbonded pdb=" OD1 ASN A 190 " pdb=" C1 NAG A 720 " model vdw 1.080 2.776 nonbonded pdb=" OG SER A 301 " pdb="CL CL A 719 " model vdw 1.951 3.270 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.082 3.040 nonbonded pdb=" OD1 ASN A 190 " pdb=" O5 NAG A 720 " model vdw 2.129 3.040 nonbonded pdb=" O PHE A 342 " pdb=" OG SER A 346 " model vdw 2.207 3.040 ... (remaining 37992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.410 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 : 0.011 0.715 4618 Z= 0.581 Angle : 1.225 65.511 6251 Z= 0.497 Chirality : 0.073 1.550 685 Planarity : 0.006 0.116 745 Dihedral : 13.320 72.021 1686 Min Nonbonded Distance : 1.080 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.14 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.02 (0.35), residues: 541 helix: 0.59 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.018 0.001 TYR A 137 PHE 0.008 0.001 PHE A 79 TRP 0.007 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.25 ( 4615) covalent geometry : angle 0.61764 / 0.35 ( 6246) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 1.46454 / 0.80 ( 2) hydrogen bonds : bond 0.22539 / 14.51 ( 273) hydrogen bonds : angle 7.59176 / 5.29 ( 807) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.71545 / 37.66 ( 1) link_NAG-ASN : angle 48.28185 / 25.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.099 Fit side-chains REVERT: A 284 ARG cc_start: 0.7029 (mmt-90) cc_final: 0.6680 (tpp80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0812 time to fit residues: 7.9998 Evaluate side-chains 65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 297 GLN A 316 ASN A 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.143978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111278 restraints weight = 5499.992| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.15 r_work: 0.3086 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4618 Z= 0.137 Angle : 0.570 7.499 6251 Z= 0.285 Chirality : 0.042 0.272 685 Planarity : 0.004 0.040 745 Dihedral : 6.404 47.192 760 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.43 % Allowed : 5.65 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.74 (0.35), residues: 541 helix: 1.22 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.14 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.016 0.001 TYR A 69 PHE 0.019 0.001 PHE A 338 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 4615) covalent geometry : angle 0.56480 / 0.28 ( 6246) SS BOND : bond 0.00189 / 0.10 ( 1) SS BOND : angle 1.66581 / 0.90 ( 2) hydrogen bonds : bond 0.04869 / 3.08 ( 273) hydrogen bonds : angle 4.99223 / 3.47 ( 807) Misc. bond : bond 0.00020 / 0.01 ( 1) link_NAG-ASN : bond 0.00326 / 0.17 ( 1) link_NAG-ASN : angle 3.35501 / 1.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.098 Fit side-chains REVERT: A 155 LYS cc_start: 0.8507 (pttm) cc_final: 0.7988 (ptmt) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.0411 time to fit residues: 4.5955 Evaluate side-chains 67 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112949 restraints weight = 5462.912| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.14 r_work: 0.3095 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4618 Z= 0.137 Angle : 0.543 7.328 6251 Z= 0.267 Chirality : 0.040 0.176 685 Planarity : 0.004 0.040 745 Dihedral : 6.091 46.349 760 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.87 % Allowed : 9.78 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.87 (0.35), residues: 541 helix: 1.32 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.07 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.017 0.001 TYR A 69 PHE 0.016 0.001 PHE A 338 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 4615) covalent geometry : angle 0.54150 / 0.27 ( 6246) SS BOND : bond 0.00148 / 0.08 ( 1) SS BOND : angle 1.36909 / 0.75 ( 2) hydrogen bonds : bond 0.04187 / 2.65 ( 273) hydrogen bonds : angle 4.69615 / 3.25 ( 807) Misc. bond : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : bond 0.00033 / 0.02 ( 1) link_NAG-ASN : angle 1.80333 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.137 Fit side-chains REVERT: A 155 LYS cc_start: 0.8485 (pttm) cc_final: 0.7986 (ptmt) REVERT: A 434 PHE cc_start: 0.8448 (t80) cc_final: 0.8219 (t80) outliers start: 4 outliers final: 1 residues processed: 78 average time/residue: 0.0427 time to fit residues: 4.7537 Evaluate side-chains 71 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN A 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109782 restraints weight = 5541.186| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.20 r_work: 0.3042 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4618 Z= 0.173 Angle : 0.561 7.279 6251 Z= 0.276 Chirality : 0.042 0.177 685 Planarity : 0.004 0.043 745 Dihedral : 6.147 46.252 760 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.87 % Allowed : 10.22 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.86 (0.35), residues: 541 helix: 1.29 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.05 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.019 0.001 TYR A 69 PHE 0.017 0.001 PHE A 338 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 4615) covalent geometry : angle 0.56043 / 0.28 ( 6246) SS BOND : bond 0.00120 / 0.06 ( 1) SS BOND : angle 1.27265 / 0.69 ( 2) hydrogen bonds : bond 0.04135 / 2.62 ( 273) hydrogen bonds : angle 4.68605 / 3.24 ( 807) Misc. bond : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : bond 0.00036 / 0.02 ( 1) link_NAG-ASN : angle 1.34611 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.130 Fit side-chains REVERT: A 155 LYS cc_start: 0.8520 (pttm) cc_final: 0.7936 (ptmt) REVERT: A 434 PHE cc_start: 0.8437 (t80) cc_final: 0.8208 (t80) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.0419 time to fit residues: 4.1146 Evaluate side-chains 68 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115441 restraints weight = 5507.833| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.16 r_work: 0.3150 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4618 Z= 0.106 Angle : 0.519 6.995 6251 Z= 0.251 Chirality : 0.039 0.180 685 Planarity : 0.004 0.043 745 Dihedral : 5.429 44.212 760 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.30 % Allowed : 10.87 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.14 (0.35), residues: 541 helix: 1.48 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.96 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.014 0.001 TYR A 69 PHE 0.018 0.001 PHE A 338 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 4615) covalent geometry : angle 0.51850 / 0.25 ( 6246) SS BOND : bond 0.00183 / 0.10 ( 1) SS BOND : angle 1.07614 / 0.60 ( 2) hydrogen bonds : bond 0.03646 / 2.28 ( 273) hydrogen bonds : angle 4.45963 / 3.07 ( 807) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00038 / 0.02 ( 1) link_NAG-ASN : angle 1.08949 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.156 Fit side-chains REVERT: A 155 LYS cc_start: 0.8260 (pttm) cc_final: 0.7265 (mmtt) REVERT: A 201 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8372 (mmm-85) REVERT: A 395 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8460 (mt) outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.0439 time to fit residues: 4.9555 Evaluate side-chains 77 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.0000 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112338 restraints weight = 5583.748| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.20 r_work: 0.3103 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4618 Z= 0.134 Angle : 0.551 7.243 6251 Z= 0.266 Chirality : 0.040 0.181 685 Planarity : 0.004 0.046 745 Dihedral : 5.413 43.393 760 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.52 % Allowed : 11.74 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.10 (0.35), residues: 541 helix: 1.52 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.05 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.017 0.001 TYR A 69 PHE 0.014 0.001 PHE A 338 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 4615) covalent geometry : angle 0.55007 / 0.27 ( 6246) SS BOND : bond 0.00262 / 0.14 ( 1) SS BOND : angle 1.56993 / 0.86 ( 2) hydrogen bonds : bond 0.03742 / 2.35 ( 273) hydrogen bonds : angle 4.50029 / 3.10 ( 807) Misc. bond : bond 0.00000 / 0.00 ( 1) link_NAG-ASN : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : angle 1.08802 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.094 Fit side-chains REVERT: A 155 LYS cc_start: 0.8331 (pttm) cc_final: 0.7884 (ptmt) REVERT: A 566 CYS cc_start: 0.8233 (m) cc_final: 0.7937 (m) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.0449 time to fit residues: 4.9550 Evaluate side-chains 76 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110949 restraints weight = 5623.883| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.21 r_work: 0.3070 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4618 Z= 0.165 Angle : 0.569 9.457 6251 Z= 0.273 Chirality : 0.041 0.180 685 Planarity : 0.004 0.042 745 Dihedral : 5.558 43.481 760 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.52 % Allowed : 12.17 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.02 (0.35), residues: 541 helix: 1.45 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.08 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.020 0.001 TYR A 69 PHE 0.012 0.001 PHE A 338 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 4615) covalent geometry : angle 0.56801 / 0.27 ( 6246) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 1.51783 / 0.83 ( 2) hydrogen bonds : bond 0.03843 / 2.42 ( 273) hydrogen bonds : angle 4.54324 / 3.13 ( 807) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00027 / 0.01 ( 1) link_NAG-ASN : angle 1.12303 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.109 Fit side-chains REVERT: A 155 LYS cc_start: 0.8366 (pttm) cc_final: 0.7906 (ptmt) REVERT: A 395 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8417 (mt) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.0445 time to fit residues: 4.8604 Evaluate side-chains 78 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.111646 restraints weight = 5611.823| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.20 r_work: 0.3080 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4618 Z= 0.135 Angle : 0.555 7.813 6251 Z= 0.266 Chirality : 0.040 0.181 685 Planarity : 0.004 0.042 745 Dihedral : 5.475 42.599 760 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.96 % Allowed : 11.96 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.06 (0.35), residues: 541 helix: 1.46 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -1.01 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.018 0.001 TYR A 69 PHE 0.012 0.001 PHE A 338 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 4615) covalent geometry : angle 0.55459 / 0.27 ( 6246) SS BOND : bond 0.00193 / 0.10 ( 1) SS BOND : angle 1.38916 / 0.77 ( 2) hydrogen bonds : bond 0.03739 / 2.34 ( 273) hydrogen bonds : angle 4.50809 / 3.11 ( 807) Misc. bond : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : angle 1.08664 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.152 Fit side-chains REVERT: A 155 LYS cc_start: 0.8350 (pttm) cc_final: 0.7890 (ptmt) REVERT: A 395 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8409 (mt) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.0432 time to fit residues: 4.6757 Evaluate side-chains 79 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.0570 chunk 48 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.0370 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113577 restraints weight = 5528.622| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.18 r_work: 0.3133 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4618 Z= 0.111 Angle : 0.552 10.407 6251 Z= 0.261 Chirality : 0.040 0.182 685 Planarity : 0.004 0.042 745 Dihedral : 5.235 40.444 760 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.96 % Allowed : 12.17 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.15 (0.35), residues: 541 helix: 1.53 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.98 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.015 0.001 TYR A 69 PHE 0.014 0.001 PHE A 338 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4615) covalent geometry : angle 0.55094 / 0.26 ( 6246) SS BOND : bond 0.00205 / 0.11 ( 1) SS BOND : angle 1.23283 / 0.69 ( 2) hydrogen bonds : bond 0.03601 / 2.24 ( 273) hydrogen bonds : angle 4.44256 / 3.06 ( 807) Misc. bond : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : bond 0.00050 / 0.03 ( 1) link_NAG-ASN : angle 1.02778 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.157 Fit side-chains REVERT: A 155 LYS cc_start: 0.8287 (pttm) cc_final: 0.7842 (ptmt) REVERT: A 395 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 504 MET cc_start: 0.8052 (mmp) cc_final: 0.7845 (mmp) REVERT: A 566 CYS cc_start: 0.8247 (m) cc_final: 0.7933 (m) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.0344 time to fit residues: 3.8715 Evaluate side-chains 80 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 0.0060 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.0570 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 overall best weight: 0.2712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114556 restraints weight = 5544.619| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.18 r_work: 0.3120 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4618 Z= 0.106 Angle : 0.554 9.760 6251 Z= 0.262 Chirality : 0.039 0.183 685 Planarity : 0.004 0.042 745 Dihedral : 5.046 37.554 760 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 12.39 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.23 (0.35), residues: 541 helix: 1.59 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.96 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.014 0.001 PHE A 338 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 4615) covalent geometry : angle 0.55324 / 0.26 ( 6246) SS BOND : bond 0.00205 / 0.11 ( 1) SS BOND : angle 1.18225 / 0.66 ( 2) hydrogen bonds : bond 0.03523 / 2.19 ( 273) hydrogen bonds : angle 4.39564 / 3.03 ( 807) Misc. bond : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 0.99693 / 0.56 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.156 Fit side-chains REVERT: A 155 LYS cc_start: 0.8284 (pttm) cc_final: 0.7832 (ptmt) REVERT: A 168 THR cc_start: 0.9114 (m) cc_final: 0.8896 (p) REVERT: A 395 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8381 (mt) REVERT: A 566 CYS cc_start: 0.8272 (m) cc_final: 0.7946 (m) outliers start: 8 outliers final: 6 residues processed: 78 average time/residue: 0.0510 time to fit residues: 5.6045 Evaluate side-chains 82 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 33 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112772 restraints weight = 5533.336| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.16 r_work: 0.3127 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4618 Z= 0.132 Angle : 0.570 9.525 6251 Z= 0.270 Chirality : 0.040 0.182 685 Planarity : 0.004 0.042 745 Dihedral : 5.127 34.748 760 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.30 % Allowed : 13.04 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.35), residues: 541 helix: 1.49 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.98 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.018 0.001 TYR A 69 PHE 0.012 0.001 PHE A 338 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 4615) covalent geometry : angle 0.56927 / 0.27 ( 6246) SS BOND : bond 0.00166 / 0.09 ( 1) SS BOND : angle 1.20005 / 0.67 ( 2) hydrogen bonds : bond 0.03657 / 2.29 ( 273) hydrogen bonds : angle 4.42261 / 3.04 ( 807) Misc. bond : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : bond 0.00031 / 0.02 ( 1) link_NAG-ASN : angle 1.00329 / 0.56 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1019.46 seconds wall clock time: 18 minutes 8.02 seconds (1088.02 seconds total)