Starting phenix.real_space_refine on Thu Jul 24 00:03:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jd9_61385/07_2025/9jd9_61385_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jd9_61385/07_2025/9jd9_61385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jd9_61385/07_2025/9jd9_61385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jd9_61385/07_2025/9jd9_61385.map" model { file = "/net/cci-nas-00/data/ceres_data/9jd9_61385/07_2025/9jd9_61385_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jd9_61385/07_2025/9jd9_61385_neut.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.060 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3067 2.51 5 N 670 2.21 5 O 757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4530 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4373 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 523} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 157 Unusual residues: {' CL': 1, ' NA': 2, 'C14': 1, 'D10': 2, 'D12': 3, 'DD9': 1, 'HEX': 1, 'HP6': 2, 'NAG': 1, 'OCT': 4, 'TAU': 1} Classifications: {'undetermined': 19, 'water': 2} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.83 Number of scatterers: 4530 At special positions: 0 Unit cell: (86.51, 66.465, 88.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 757 8.00 N 670 7.00 C 3067 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 Atom "HETATM 4526 O5 NAG A 719 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A 719 " - " ASN A 190 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 822.5 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 77.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.572A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.803A 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 106 removed outlier: 6.164A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.071A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.782A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 removed outlier: 4.366A pdb=" N LYS A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 245 through 266 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 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.240A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.890A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.637A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.565A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.773A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.561A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 4.168A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) 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 450 through 462 removed outlier: 3.733A 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 497 removed outlier: 3.976A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.501A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.076A 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 581 removed outlier: 3.686A pdb=" N THR A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 281 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 883 1.33 - 1.45: 1174 1.45 - 1.57: 2549 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 4653 Sorted by residual: bond pdb=" O2 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.477 1.547 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N THR A 596 " pdb=" CA THR A 596 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.96e+00 bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.75e+00 bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.75e+00 bond pdb=" N GLU A 591 " pdb=" CA GLU A 591 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.44e+00 ... (remaining 4648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 6045 1.40 - 2.80: 189 2.80 - 4.21: 41 4.21 - 5.61: 14 5.61 - 7.01: 2 Bond angle restraints: 6291 Sorted by residual: angle pdb=" CA GLY A 209 " pdb=" C GLY A 209 " pdb=" O GLY A 209 " ideal model delta sigma weight residual 121.60 118.12 3.48 9.70e-01 1.06e+00 1.29e+01 angle pdb=" CA ARG A 583 " pdb=" C ARG A 583 " pdb=" O ARG A 583 " ideal model delta sigma weight residual 122.51 118.01 4.50 1.34e+00 5.57e-01 1.13e+01 angle pdb=" CA ASN A 586 " pdb=" C ASN A 586 " pdb=" O ASN A 586 " ideal model delta sigma weight residual 122.63 118.34 4.29 1.29e+00 6.01e-01 1.11e+01 angle pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" O VAL A 203 " ideal model delta sigma weight residual 120.85 117.35 3.50 1.06e+00 8.90e-01 1.09e+01 angle pdb=" N SER A 205 " pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 111.39 107.13 4.26 1.38e+00 5.25e-01 9.51e+00 ... (remaining 6286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 2343 15.00 - 29.99: 249 29.99 - 44.99: 56 44.99 - 59.99: 15 59.99 - 74.98: 4 Dihedral angle restraints: 2667 sinusoidal: 1079 harmonic: 1588 Sorted by residual: dihedral pdb=" CA PHE A 392 " pdb=" C PHE A 392 " pdb=" N ILE A 393 " pdb=" CA ILE A 393 " ideal model delta harmonic sigma weight residual 180.00 164.08 15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CB MET A 380 " pdb=" CG MET A 380 " pdb=" SD MET A 380 " pdb=" CE MET A 380 " ideal model delta sinusoidal sigma weight residual 180.00 123.23 56.77 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB MET A 327 " pdb=" CG MET A 327 " pdb=" SD MET A 327 " pdb=" CE MET A 327 " ideal model delta sinusoidal sigma weight residual 60.00 112.58 -52.58 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 2664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 595 0.062 - 0.124: 78 0.124 - 0.185: 10 0.185 - 0.247: 0 0.247 - 0.309: 1 Chirality restraints: 684 Sorted by residual: chirality pdb=" C1 NAG A 719 " pdb=" ND2 ASN A 190 " pdb=" C2 NAG A 719 " pdb=" O5 NAG A 719 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-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 2.61 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 681 not shown) Planarity restraints: 755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.121 2.00e-02 2.50e+03 1.40e-01 2.44e+02 pdb=" CG ASN A 190 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG A 719 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 719 " -0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG A 719 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 719 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 719 " 0.057 2.00e-02 2.50e+03 pdb=" O7 NAG A 719 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C LEU A 87 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 87 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 88 " 0.012 2.00e-02 2.50e+03 ... (remaining 752 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 64 2.67 - 3.22: 4379 3.22 - 3.78: 7123 3.78 - 4.34: 10196 4.34 - 4.90: 16875 Nonbonded interactions: 38637 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.107 3.040 nonbonded pdb=" OG SER A 301 " pdb="NA NA A 717 " model vdw 2.228 2.470 nonbonded pdb=" O SER A 301 " pdb="NA NA A 717 " model vdw 2.235 2.470 nonbonded pdb=" O2 TAU A 701 " pdb="NA NA A 717 " model vdw 2.245 2.470 nonbonded pdb=" OD2 ASP A 401 " pdb=" O HOH A 801 " model vdw 2.254 3.040 ... (remaining 38632 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: 1.200 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 0.683 4656 Z= 1.039 Angle : 0.812 36.743 6296 Z= 0.409 Chirality : 0.045 0.309 684 Planarity : 0.005 0.062 754 Dihedral : 13.108 74.983 1658 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.43 % Allowed : 0.21 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.35), residues: 548 helix: 0.28 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.67 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 113 HIS 0.001 0.000 HIS A 212 PHE 0.020 0.001 PHE A 58 TYR 0.015 0.001 TYR A 137 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.04799 ( 1) link_NAG-ASN : angle 24.25370 ( 3) hydrogen bonds : bond 0.21745 ( 281) hydrogen bonds : angle 7.76372 ( 828) SS BOND : bond 0.00141 ( 1) SS BOND : angle 1.58395 ( 2) covalent geometry : bond 0.00484 ( 4653) covalent geometry : angle 0.61515 ( 6291) Misc. bond : bond 0.68259 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.562 Fit side-chains REVERT: A 179 ASN cc_start: 0.6055 (t0) cc_final: 0.5786 (t0) REVERT: A 202 ASN cc_start: 0.8454 (t0) cc_final: 0.8213 (t0) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.1474 time to fit residues: 13.1347 Evaluate side-chains 58 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 297 GLN A 333 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.088923 restraints weight = 5566.821| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.04 r_work: 0.2758 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4656 Z= 0.154 Angle : 0.585 9.070 6296 Z= 0.294 Chirality : 0.041 0.145 684 Planarity : 0.005 0.039 754 Dihedral : 7.258 50.343 711 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.93 % Allowed : 4.93 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.35), residues: 548 helix: 0.97 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.89 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 470 HIS 0.005 0.001 HIS A 170 PHE 0.018 0.001 PHE A 58 TYR 0.025 0.002 TYR A 137 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 1) link_NAG-ASN : angle 4.67674 ( 3) hydrogen bonds : bond 0.04883 ( 281) hydrogen bonds : angle 5.04528 ( 828) SS BOND : bond 0.00864 ( 1) SS BOND : angle 3.68598 ( 2) covalent geometry : bond 0.00351 ( 4653) covalent geometry : angle 0.57256 ( 6291) Misc. bond : bond 0.00163 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.546 Fit side-chains REVERT: A 107 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 179 ASN cc_start: 0.6367 (t0) cc_final: 0.6103 (t0) REVERT: A 202 ASN cc_start: 0.8553 (t0) cc_final: 0.8272 (t0) REVERT: A 587 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.7209 (ttp-110) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.1562 time to fit residues: 13.9539 Evaluate side-chains 65 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.089904 restraints weight = 5537.537| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.07 r_work: 0.2768 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4656 Z= 0.128 Angle : 0.529 9.531 6296 Z= 0.263 Chirality : 0.039 0.144 684 Planarity : 0.004 0.041 754 Dihedral : 6.964 54.806 711 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 7.92 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.35), residues: 548 helix: 1.33 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.86 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 170 PHE 0.033 0.001 PHE A 58 TYR 0.026 0.001 TYR A 137 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 1) link_NAG-ASN : angle 3.53301 ( 3) hydrogen bonds : bond 0.04087 ( 281) hydrogen bonds : angle 4.66617 ( 828) SS BOND : bond 0.00616 ( 1) SS BOND : angle 2.41035 ( 2) covalent geometry : bond 0.00288 ( 4653) covalent geometry : angle 0.52168 ( 6291) Misc. bond : bond 0.00196 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8391 (p90) REVERT: A 172 MET cc_start: 0.7559 (tpt) cc_final: 0.7354 (tpt) REVERT: A 179 ASN cc_start: 0.6425 (t0) cc_final: 0.6146 (t0) REVERT: A 202 ASN cc_start: 0.8483 (t0) cc_final: 0.8168 (t0) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.1348 time to fit residues: 11.5255 Evaluate side-chains 61 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.090270 restraints weight = 5564.790| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.03 r_work: 0.2770 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4656 Z= 0.127 Angle : 0.519 9.425 6296 Z= 0.259 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.830 59.622 711 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.36 % Allowed : 10.28 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.35), residues: 548 helix: 1.44 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.79 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.011 0.001 PHE A 58 TYR 0.025 0.001 TYR A 137 ARG 0.001 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 3.42064 ( 3) hydrogen bonds : bond 0.03873 ( 281) hydrogen bonds : angle 4.54185 ( 828) SS BOND : bond 0.00368 ( 1) SS BOND : angle 1.76436 ( 2) covalent geometry : bond 0.00290 ( 4653) covalent geometry : angle 0.51332 ( 6291) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8255 (p90) REVERT: A 179 ASN cc_start: 0.6286 (t0) cc_final: 0.6010 (t0) REVERT: A 202 ASN cc_start: 0.8510 (t0) cc_final: 0.8182 (t0) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.1523 time to fit residues: 13.6224 Evaluate side-chains 65 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.097470 restraints weight = 5608.193| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.89 r_work: 0.2824 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4656 Z= 0.151 Angle : 0.530 9.527 6296 Z= 0.264 Chirality : 0.040 0.145 684 Planarity : 0.004 0.043 754 Dihedral : 6.896 56.007 711 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.78 % Allowed : 10.28 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.35), residues: 548 helix: 1.45 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.79 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.014 0.001 PHE A 58 TYR 0.025 0.001 TYR A 137 ARG 0.001 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 3.37259 ( 3) hydrogen bonds : bond 0.03973 ( 281) hydrogen bonds : angle 4.57548 ( 828) SS BOND : bond 0.00367 ( 1) SS BOND : angle 1.91140 ( 2) covalent geometry : bond 0.00357 ( 4653) covalent geometry : angle 0.52412 ( 6291) Misc. bond : bond 0.00138 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8038 (p90) REVERT: A 179 ASN cc_start: 0.6368 (t0) cc_final: 0.6089 (t0) REVERT: A 202 ASN cc_start: 0.8501 (t0) cc_final: 0.8131 (t0) outliers start: 13 outliers final: 11 residues processed: 63 average time/residue: 0.1294 time to fit residues: 11.2849 Evaluate side-chains 66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.094382 restraints weight = 5541.408| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.04 r_work: 0.2795 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4656 Z= 0.106 Angle : 0.498 9.425 6296 Z= 0.247 Chirality : 0.038 0.143 684 Planarity : 0.004 0.043 754 Dihedral : 6.528 57.284 711 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.36 % Allowed : 10.71 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.35), residues: 548 helix: 1.61 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.77 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.010 0.001 PHE A 474 TYR 0.025 0.001 TYR A 137 ARG 0.001 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00050 ( 1) link_NAG-ASN : angle 3.33000 ( 3) hydrogen bonds : bond 0.03585 ( 281) hydrogen bonds : angle 4.38587 ( 828) SS BOND : bond 0.00383 ( 1) SS BOND : angle 1.30581 ( 2) covalent geometry : bond 0.00231 ( 4653) covalent geometry : angle 0.49217 ( 6291) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7970 (p90) REVERT: A 179 ASN cc_start: 0.6445 (t0) cc_final: 0.6154 (t0) REVERT: A 202 ASN cc_start: 0.8536 (t0) cc_final: 0.8215 (t0) REVERT: A 442 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8186 (tp) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.1292 time to fit residues: 11.8681 Evaluate side-chains 67 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.119388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.090863 restraints weight = 5527.816| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.07 r_work: 0.2766 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4656 Z= 0.132 Angle : 0.514 9.437 6296 Z= 0.256 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.613 59.102 711 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.57 % Allowed : 11.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.35), residues: 548 helix: 1.58 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.73 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 PHE 0.012 0.001 PHE A 58 TYR 0.025 0.001 TYR A 137 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 3.37329 ( 3) hydrogen bonds : bond 0.03730 ( 281) hydrogen bonds : angle 4.43985 ( 828) SS BOND : bond 0.00326 ( 1) SS BOND : angle 1.66470 ( 2) covalent geometry : bond 0.00308 ( 4653) covalent geometry : angle 0.50787 ( 6291) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.501 Fit side-chains REVERT: A 179 ASN cc_start: 0.6570 (t0) cc_final: 0.6280 (t0) REVERT: A 202 ASN cc_start: 0.8610 (t0) cc_final: 0.8292 (t0) REVERT: A 442 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8322 (tp) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.1335 time to fit residues: 11.9742 Evaluate side-chains 66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103849 restraints weight = 5469.879| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.86 r_work: 0.2832 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4656 Z= 0.116 Angle : 0.504 9.423 6296 Z= 0.251 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.514 59.950 711 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 12.42 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.36), residues: 548 helix: 1.68 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.73 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.010 0.001 PHE A 474 TYR 0.025 0.001 TYR A 137 ARG 0.001 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 3.35709 ( 3) hydrogen bonds : bond 0.03620 ( 281) hydrogen bonds : angle 4.39549 ( 828) SS BOND : bond 0.00353 ( 1) SS BOND : angle 1.41061 ( 2) covalent geometry : bond 0.00263 ( 4653) covalent geometry : angle 0.49842 ( 6291) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.479 Fit side-chains REVERT: A 179 ASN cc_start: 0.6443 (t0) cc_final: 0.6145 (t0) REVERT: A 202 ASN cc_start: 0.8469 (t0) cc_final: 0.8126 (t0) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.1315 time to fit residues: 11.1265 Evaluate side-chains 64 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105787 restraints weight = 5392.511| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.83 r_work: 0.3011 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4656 Z= 0.124 Angle : 0.513 9.466 6296 Z= 0.255 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.512 59.214 711 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 12.42 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.36), residues: 548 helix: 1.67 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.73 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.012 0.001 PHE A 50 TYR 0.024 0.001 TYR A 137 ARG 0.001 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00002 ( 1) link_NAG-ASN : angle 3.39569 ( 3) hydrogen bonds : bond 0.03655 ( 281) hydrogen bonds : angle 4.44400 ( 828) SS BOND : bond 0.00310 ( 1) SS BOND : angle 1.52767 ( 2) covalent geometry : bond 0.00284 ( 4653) covalent geometry : angle 0.50672 ( 6291) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.462 Fit side-chains REVERT: A 179 ASN cc_start: 0.6769 (t0) cc_final: 0.6499 (t0) REVERT: A 202 ASN cc_start: 0.8572 (t0) cc_final: 0.8295 (t0) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.1377 time to fit residues: 11.7850 Evaluate side-chains 65 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.0030 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.102629 restraints weight = 5491.095| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.76 r_work: 0.3031 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4656 Z= 0.145 Angle : 0.528 9.464 6296 Z= 0.264 Chirality : 0.040 0.145 684 Planarity : 0.004 0.043 754 Dihedral : 6.756 56.888 711 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.93 % Allowed : 12.63 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.35), residues: 548 helix: 1.59 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.68 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.014 0.001 PHE A 58 TYR 0.024 0.001 TYR A 69 ARG 0.001 0.000 ARG A 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 1) link_NAG-ASN : angle 3.35910 ( 3) hydrogen bonds : bond 0.03829 ( 281) hydrogen bonds : angle 4.50419 ( 828) SS BOND : bond 0.00300 ( 1) SS BOND : angle 1.85019 ( 2) covalent geometry : bond 0.00342 ( 4653) covalent geometry : angle 0.52212 ( 6291) Misc. bond : bond 0.00114 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.524 Fit side-chains REVERT: A 107 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7744 (tt0) REVERT: A 179 ASN cc_start: 0.6821 (t0) cc_final: 0.6571 (t0) REVERT: A 202 ASN cc_start: 0.8670 (t0) cc_final: 0.8397 (t0) outliers start: 9 outliers final: 9 residues processed: 61 average time/residue: 0.1352 time to fit residues: 11.4525 Evaluate side-chains 64 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103602 restraints weight = 5478.865| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.77 r_work: 0.3007 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4656 Z= 0.128 Angle : 0.515 9.489 6296 Z= 0.257 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.634 56.399 711 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.14 % Allowed : 12.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.36), residues: 548 helix: 1.65 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.70 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.012 0.001 PHE A 50 TYR 0.023 0.001 TYR A 137 ARG 0.001 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00009 ( 1) link_NAG-ASN : angle 3.35618 ( 3) hydrogen bonds : bond 0.03688 ( 281) hydrogen bonds : angle 4.44208 ( 828) SS BOND : bond 0.00328 ( 1) SS BOND : angle 1.53561 ( 2) covalent geometry : bond 0.00295 ( 4653) covalent geometry : angle 0.50966 ( 6291) Misc. bond : bond 0.00113 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2628.53 seconds wall clock time: 46 minutes 34.69 seconds (2794.69 seconds total)