Starting phenix.real_space_refine on Thu Jul 2 00:23:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdg_61392/07_2026/9jdg_61392_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdg_61392/07_2026/9jdg_61392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jdg_61392/07_2026/9jdg_61392_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdg_61392/07_2026/9jdg_61392_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jdg_61392/07_2026/9jdg_61392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdg_61392/07_2026/9jdg_61392.map" } resolution = 3.23 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= 0.049 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 3021 2.51 5 N 655 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4459 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: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 147 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 5, 'D12': 3, 'NAG': 1, 'OCT': 5} Classifications: {'undetermined': 14, 'water': 7} Link IDs: {None: 19} 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: 1.37, per 1000 atoms: 0.31 Number of scatterers: 4459 At special positions: 0 Unit cell: (87.565, 67.52, 88.62, 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 750 8.00 N 655 7.00 C 3021 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=0, symmetry=0 Links applied NAG-ASN " NAG A 715 " - " ASN A 190 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 188.2 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: 32 helices and 1 sheets defined 77.6% 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: 3.616A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 4.080A 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 108 through 117 removed outlier: 4.238A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.347A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 removed outlier: 4.595A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.526A 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 removed outlier: 3.563A pdb=" N VAL A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 266 removed outlier: 4.046A 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 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.708A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.522A pdb=" N ILE A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.551A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.798A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.641A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.568A pdb=" N GLY A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 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: 4.043A 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 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.563A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.960A 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 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 274 hydrogen bonds defined for protein. 816 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: 0.56 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1257 1.34 - 1.46: 957 1.46 - 1.57: 2319 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4579 Sorted by residual: bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.46e+00 bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.21e+00 bond pdb=" N PHE A 191 " pdb=" CA PHE A 191 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.17e+00 bond pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.27e-02 6.20e+03 8.13e+00 bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 ... (remaining 4574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 5956 1.52 - 3.04: 207 3.04 - 4.56: 25 4.56 - 6.08: 6 6.08 - 7.59: 3 Bond angle restraints: 6197 Sorted by residual: angle pdb=" CA GLY A 594 " pdb=" C GLY A 594 " pdb=" O GLY A 594 " ideal model delta sigma weight residual 121.58 118.17 3.41 9.00e-01 1.23e+00 1.44e+01 angle pdb=" CA ARG A 587 " pdb=" C ARG A 587 " pdb=" O ARG A 587 " ideal model delta sigma weight residual 122.63 118.06 4.57 1.29e+00 6.01e-01 1.26e+01 angle pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" O VAL A 203 " ideal model delta sigma weight residual 121.05 117.51 3.54 1.11e+00 8.12e-01 1.02e+01 angle pdb=" CA SER A 205 " pdb=" C SER A 205 " pdb=" O SER A 205 " ideal model delta sigma weight residual 122.14 118.31 3.83 1.24e+00 6.50e-01 9.53e+00 angle pdb=" N SER A 205 " pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 111.24 106.99 4.25 1.38e+00 5.25e-01 9.48e+00 ... (remaining 6192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 2328 16.12 - 32.24: 222 32.24 - 48.36: 55 48.36 - 64.48: 10 64.48 - 80.60: 4 Dihedral angle restraints: 2619 sinusoidal: 1051 harmonic: 1568 Sorted by residual: dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TRP A 166 " pdb=" C TRP A 166 " pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+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 -125.19 -54.81 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 2616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 662 0.112 - 0.224: 14 0.224 - 0.336: 0 0.336 - 0.448: 0 0.448 - 0.560: 1 Chirality restraints: 677 Sorted by residual: chirality pdb=" C1 NAG A 715 " pdb=" ND2 ASN A 190 " pdb=" C2 NAG A 715 " pdb=" O5 NAG A 715 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.85e+00 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 8.66e-01 chirality pdb=" CA VAL A 590 " pdb=" N VAL A 590 " pdb=" C VAL A 590 " pdb=" CB VAL A 590 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 674 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.161 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" CG ASN A 190 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.335 2.00e-02 2.50e+03 pdb=" C1 NAG A 715 " -0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 715 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG A 715 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 715 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 715 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A 715 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 587 " -0.158 9.50e-02 1.11e+02 7.10e-02 3.10e+00 pdb=" NE ARG A 587 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 587 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 587 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 587 " -0.005 2.00e-02 2.50e+03 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 60 2.67 - 3.23: 4352 3.23 - 3.78: 6909 3.78 - 4.34: 9759 4.34 - 4.90: 16317 Nonbonded interactions: 37397 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.109 3.040 nonbonded pdb=" ND2 ASN A 190 " pdb=" N2 NAG A 715 " model vdw 2.113 2.560 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.275 3.120 nonbonded pdb=" NE2 GLN A 289 " pdb=" OD1 ASP A 293 " model vdw 2.280 3.120 nonbonded pdb=" O ALA A 433 " pdb=" OG SER A 437 " model vdw 2.356 3.040 ... (remaining 37392 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: 1.010 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.190 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.006 0.177 4581 Z= 0.316 Angle : 0.839 33.872 6202 Z= 0.431 Chirality : 0.047 0.560 677 Planarity : 0.006 0.071 745 Dihedral : 13.695 80.598 1624 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.22 % Allowed : 0.43 % Favored : 99.35 % 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: -0.46 (0.35), residues: 541 helix: 0.21 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 564 TYR 0.019 0.001 TYR A 578 PHE 0.017 0.001 PHE A 95 TRP 0.013 0.001 TRP A 470 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.29 ( 4579) covalent geometry : angle 0.65574 / 0.39 ( 6197) SS BOND : bond 0.00160 / 0.08 ( 1) SS BOND : angle 1.97443 / 1.08 ( 2) hydrogen bonds : bond 0.23369 / 15.28 ( 274) hydrogen bonds : angle 7.71198 / 5.47 ( 816) link_NAG-ASN : bond 0.17731 / 9.33 ( 1) link_NAG-ASN : angle 23.72417 / 12.52 ( 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 58 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.7703 (mmp) cc_final: 0.7380 (mmp) REVERT: A 427 ARG cc_start: 0.7043 (mtm180) cc_final: 0.6096 (mtm180) REVERT: A 460 TYR cc_start: 0.8990 (t80) cc_final: 0.8752 (t80) REVERT: A 566 CYS cc_start: 0.8157 (m) cc_final: 0.7941 (m) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0658 time to fit residues: 5.0468 Evaluate side-chains 49 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 GLN A 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.093588 restraints weight = 5493.519| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.75 r_work: 0.2810 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4581 Z= 0.143 Angle : 0.548 7.498 6202 Z= 0.284 Chirality : 0.039 0.124 677 Planarity : 0.004 0.038 745 Dihedral : 5.941 42.807 698 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.87 % Allowed : 6.96 % Favored : 92.17 % 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: 0.53 (0.35), residues: 541 helix: 1.02 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.25 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.013 0.001 TYR A 69 PHE 0.013 0.001 PHE A 338 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4579) covalent geometry : angle 0.54583 / 0.28 ( 6197) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 1.54714 / 0.84 ( 2) hydrogen bonds : bond 0.05106 / 3.14 ( 274) hydrogen bonds : angle 4.90318 / 3.33 ( 816) link_NAG-ASN : bond 0.00503 / 0.26 ( 1) link_NAG-ASN : angle 1.69915 / 0.98 ( 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 66 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.157 Fit side-chains REVERT: A 309 MET cc_start: 0.7604 (mmp) cc_final: 0.7347 (mmp) REVERT: A 351 MET cc_start: 0.8619 (mtp) cc_final: 0.8341 (mtm) REVERT: A 406 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8312 (mm-30) REVERT: A 427 ARG cc_start: 0.6958 (mtm180) cc_final: 0.6239 (mtm180) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 0.0557 time to fit residues: 4.8824 Evaluate side-chains 55 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.120226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.094232 restraints weight = 5543.836| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.67 r_work: 0.2839 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4581 Z= 0.140 Angle : 0.519 7.181 6202 Z= 0.264 Chirality : 0.039 0.124 677 Planarity : 0.004 0.034 745 Dihedral : 5.685 33.138 698 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.30 % Allowed : 9.57 % Favored : 89.13 % 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: 0.77 (0.35), residues: 541 helix: 1.24 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.27 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.029 0.001 TYR A 460 PHE 0.012 0.001 PHE A 474 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 4579) covalent geometry : angle 0.51770 / 0.26 ( 6197) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 1.41987 / 0.76 ( 2) hydrogen bonds : bond 0.04419 / 2.74 ( 274) hydrogen bonds : angle 4.60200 / 3.11 ( 816) link_NAG-ASN : bond 0.00055 / 0.03 ( 1) link_NAG-ASN : angle 1.02119 / 0.59 ( 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 60 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.180 Fit side-chains REVERT: A 309 MET cc_start: 0.7649 (mmp) cc_final: 0.7427 (mmp) REVERT: A 406 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8210 (mm-30) REVERT: A 427 ARG cc_start: 0.6882 (mtm180) cc_final: 0.6192 (mtm180) REVERT: A 577 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7848 (tppt) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.0592 time to fit residues: 4.5468 Evaluate side-chains 55 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 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 = 0.3288 r_free = 0.3288 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.094775 restraints weight = 5574.825| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.75 r_work: 0.2834 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4581 Z= 0.125 Angle : 0.498 7.045 6202 Z= 0.252 Chirality : 0.038 0.121 677 Planarity : 0.004 0.033 745 Dihedral : 5.426 33.808 698 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.17 % Allowed : 9.57 % Favored : 88.26 % 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: 1.08 (0.35), residues: 541 helix: 1.50 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.24 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.023 0.001 TYR A 460 PHE 0.011 0.001 PHE A 474 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 4579) covalent geometry : angle 0.49761 / 0.25 ( 6197) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 1.10560 / 0.60 ( 2) hydrogen bonds : bond 0.03970 / 2.47 ( 274) hydrogen bonds : angle 4.40277 / 2.97 ( 816) link_NAG-ASN : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : angle 0.92625 / 0.52 ( 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 68 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.138 Fit side-chains REVERT: A 172 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7219 (ttm) REVERT: A 176 MET cc_start: 0.8564 (mtp) cc_final: 0.8083 (mtp) REVERT: A 321 ASN cc_start: 0.8201 (t0) cc_final: 0.7752 (t0) REVERT: A 351 MET cc_start: 0.8710 (mtp) cc_final: 0.8477 (mtm) REVERT: A 406 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8234 (mm-30) REVERT: A 427 ARG cc_start: 0.6923 (mtm180) cc_final: 0.6235 (mtm180) REVERT: A 577 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7800 (tppt) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.0565 time to fit residues: 4.9289 Evaluate side-chains 61 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.0570 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.0470 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.123771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.096281 restraints weight = 5511.417| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.82 r_work: 0.2851 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4581 Z= 0.105 Angle : 0.479 7.021 6202 Z= 0.241 Chirality : 0.037 0.118 677 Planarity : 0.004 0.032 745 Dihedral : 5.153 35.537 698 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.30 % Allowed : 12.17 % Favored : 86.52 % 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: 1.39 (0.36), residues: 541 helix: 1.79 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.32 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.019 0.001 TYR A 460 PHE 0.010 0.001 PHE A 474 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 4579) covalent geometry : angle 0.47817 / 0.24 ( 6197) SS BOND : bond 0.00179 / 0.09 ( 1) SS BOND : angle 1.08017 / 0.58 ( 2) hydrogen bonds : bond 0.03660 / 2.26 ( 274) hydrogen bonds : angle 4.27437 / 2.88 ( 816) link_NAG-ASN : bond 0.00059 / 0.03 ( 1) link_NAG-ASN : angle 0.89035 / 0.49 ( 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 66 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.131 Fit side-chains REVERT: A 172 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7088 (ttm) REVERT: A 176 MET cc_start: 0.8579 (mtp) cc_final: 0.8100 (mtp) REVERT: A 292 ILE cc_start: 0.8078 (mm) cc_final: 0.7838 (mt) REVERT: A 321 ASN cc_start: 0.8179 (t0) cc_final: 0.7701 (t0) REVERT: A 406 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8175 (mm-30) REVERT: A 427 ARG cc_start: 0.6905 (mtm180) cc_final: 0.6222 (mtm180) REVERT: A 577 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7616 (tppt) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.0430 time to fit residues: 3.7445 Evaluate side-chains 64 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.124153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.096233 restraints weight = 5665.893| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.85 r_work: 0.2836 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4581 Z= 0.119 Angle : 0.489 7.011 6202 Z= 0.245 Chirality : 0.038 0.125 677 Planarity : 0.003 0.031 745 Dihedral : 5.160 37.034 698 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 11.96 % 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: 1.48 (0.36), residues: 541 helix: 1.87 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.31 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.023 0.001 TYR A 460 PHE 0.011 0.001 PHE A 474 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 4579) covalent geometry : angle 0.48792 / 0.24 ( 6197) SS BOND : bond 0.00132 / 0.07 ( 1) SS BOND : angle 1.29885 / 0.70 ( 2) hydrogen bonds : bond 0.03704 / 2.30 ( 274) hydrogen bonds : angle 4.26639 / 2.87 ( 816) link_NAG-ASN : bond 0.00048 / 0.03 ( 1) link_NAG-ASN : angle 0.86560 / 0.48 ( 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 66 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7153 (ttm) REVERT: A 176 MET cc_start: 0.8587 (mtp) cc_final: 0.8122 (mtp) REVERT: A 292 ILE cc_start: 0.8118 (mm) cc_final: 0.7897 (mt) REVERT: A 321 ASN cc_start: 0.8167 (t0) cc_final: 0.7696 (t0) REVERT: A 427 ARG cc_start: 0.6889 (mtm180) cc_final: 0.6196 (mtm180) REVERT: A 494 ASP cc_start: 0.8670 (t70) cc_final: 0.8399 (t0) REVERT: A 577 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7659 (tppt) outliers start: 8 outliers final: 7 residues processed: 62 average time/residue: 0.0503 time to fit residues: 4.1300 Evaluate side-chains 63 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.123012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.095205 restraints weight = 5653.161| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.84 r_work: 0.2828 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4581 Z= 0.132 Angle : 0.498 6.982 6202 Z= 0.249 Chirality : 0.038 0.127 677 Planarity : 0.004 0.032 745 Dihedral : 5.273 38.393 698 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.17 % Allowed : 11.96 % 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: 1.46 (0.36), residues: 541 helix: 1.86 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.32 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.020 0.001 TYR A 460 PHE 0.013 0.001 PHE A 474 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 4579) covalent geometry : angle 0.49731 / 0.25 ( 6197) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 1.33537 / 0.72 ( 2) hydrogen bonds : bond 0.03765 / 2.33 ( 274) hydrogen bonds : angle 4.28022 / 2.88 ( 816) link_NAG-ASN : bond 0.00042 / 0.02 ( 1) link_NAG-ASN : angle 0.83856 / 0.46 ( 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 65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7123 (ttm) REVERT: A 176 MET cc_start: 0.8586 (mtp) cc_final: 0.8133 (mtp) REVERT: A 321 ASN cc_start: 0.8164 (t0) cc_final: 0.7681 (t0) REVERT: A 427 ARG cc_start: 0.6851 (mtm180) cc_final: 0.6190 (mtm180) REVERT: A 494 ASP cc_start: 0.8650 (t70) cc_final: 0.8347 (t0) REVERT: A 577 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7548 (tppt) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.0524 time to fit residues: 4.3857 Evaluate side-chains 61 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.123685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095827 restraints weight = 5624.876| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.86 r_work: 0.2839 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4581 Z= 0.121 Angle : 0.489 7.000 6202 Z= 0.244 Chirality : 0.038 0.119 677 Planarity : 0.003 0.032 745 Dihedral : 5.193 38.422 698 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.17 % Allowed : 12.61 % Favored : 85.22 % 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: 1.56 (0.36), residues: 541 helix: 1.95 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.020 0.001 TYR A 460 PHE 0.012 0.001 PHE A 404 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 4579) covalent geometry : angle 0.48846 / 0.24 ( 6197) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 1.26681 / 0.68 ( 2) hydrogen bonds : bond 0.03635 / 2.24 ( 274) hydrogen bonds : angle 4.23736 / 2.85 ( 816) link_NAG-ASN : bond 0.00058 / 0.03 ( 1) link_NAG-ASN : angle 0.84631 / 0.47 ( 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 65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7142 (ttm) REVERT: A 176 MET cc_start: 0.8551 (mtp) cc_final: 0.8104 (mtp) REVERT: A 321 ASN cc_start: 0.8183 (t0) cc_final: 0.7714 (t0) REVERT: A 427 ARG cc_start: 0.6888 (mtm180) cc_final: 0.6221 (mtm180) REVERT: A 494 ASP cc_start: 0.8659 (t70) cc_final: 0.8357 (t0) REVERT: A 577 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7558 (tppt) outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 0.0471 time to fit residues: 3.9299 Evaluate side-chains 65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 30 optimal weight: 0.0050 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4010 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.124391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.096917 restraints weight = 5591.229| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.84 r_work: 0.2862 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4581 Z= 0.107 Angle : 0.477 6.972 6202 Z= 0.238 Chirality : 0.037 0.116 677 Planarity : 0.003 0.031 745 Dihedral : 5.010 38.318 698 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.74 % Allowed : 12.61 % 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: 1.69 (0.36), residues: 541 helix: 2.06 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.31 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.018 0.001 TYR A 460 PHE 0.010 0.001 PHE A 474 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 0.00246 / 0.11 ( 4579) covalent geometry : angle 0.47618 / 0.24 ( 6197) SS BOND : bond 0.00115 / 0.06 ( 1) SS BOND : angle 1.22371 / 0.66 ( 2) hydrogen bonds : bond 0.03463 / 2.13 ( 274) hydrogen bonds : angle 4.15115 / 2.78 ( 816) link_NAG-ASN : bond 0.00072 / 0.04 ( 1) link_NAG-ASN : angle 0.89442 / 0.50 ( 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 64 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7120 (ttm) REVERT: A 176 MET cc_start: 0.8533 (mtp) cc_final: 0.8109 (mtp) REVERT: A 321 ASN cc_start: 0.8172 (t0) cc_final: 0.7708 (t0) REVERT: A 427 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6229 (mtm180) REVERT: A 494 ASP cc_start: 0.8642 (t70) cc_final: 0.8345 (t0) REVERT: A 577 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7601 (tppt) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.0461 time to fit residues: 3.7895 Evaluate side-chains 60 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.120955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.095149 restraints weight = 5608.658| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.67 r_work: 0.2865 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4581 Z= 0.143 Angle : 0.503 6.547 6202 Z= 0.252 Chirality : 0.038 0.123 677 Planarity : 0.003 0.032 745 Dihedral : 5.322 38.304 698 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.52 % Allowed : 13.48 % Favored : 85.00 % 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: 1.52 (0.36), residues: 541 helix: 1.88 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.020 0.001 TYR A 460 PHE 0.013 0.001 PHE A 474 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 4579) covalent geometry : angle 0.50220 / 0.25 ( 6197) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 1.37801 / 0.74 ( 2) hydrogen bonds : bond 0.03769 / 2.34 ( 274) hydrogen bonds : angle 4.23310 / 2.85 ( 816) link_NAG-ASN : bond 0.00060 / 0.03 ( 1) link_NAG-ASN : angle 0.86338 / 0.47 ( 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 60 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7284 (ttm) REVERT: A 176 MET cc_start: 0.8598 (mtp) cc_final: 0.8107 (mtp) REVERT: A 321 ASN cc_start: 0.8246 (t0) cc_final: 0.7819 (t0) REVERT: A 427 ARG cc_start: 0.7024 (mtm180) cc_final: 0.6349 (mtm180) REVERT: A 494 ASP cc_start: 0.8650 (t70) cc_final: 0.8353 (t0) REVERT: A 577 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7709 (tppt) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.0511 time to fit residues: 4.0493 Evaluate side-chains 59 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.120907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.095145 restraints weight = 5603.163| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.66 r_work: 0.2873 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4581 Z= 0.141 Angle : 0.503 6.258 6202 Z= 0.252 Chirality : 0.038 0.128 677 Planarity : 0.003 0.033 745 Dihedral : 5.419 39.545 698 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.52 % Allowed : 13.70 % Favored : 84.78 % 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: 1.55 (0.36), residues: 541 helix: 1.89 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.15 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.021 0.001 TYR A 460 PHE 0.013 0.001 PHE A 474 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 0.00339 / 0.14 ( 4579) covalent geometry : angle 0.50253 / 0.25 ( 6197) SS BOND : bond 0.00102 / 0.05 ( 1) SS BOND : angle 1.42039 / 0.76 ( 2) hydrogen bonds : bond 0.03762 / 2.32 ( 274) hydrogen bonds : angle 4.24222 / 2.86 ( 816) link_NAG-ASN : bond 0.00052 / 0.03 ( 1) link_NAG-ASN : angle 0.86406 / 0.48 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1033.95 seconds wall clock time: 18 minutes 27.48 seconds (1107.48 seconds total)