Starting phenix.real_space_refine on Wed Sep 17 05:02:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jd9_61385/09_2025/9jd9_61385_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jd9_61385/09_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_61385/09_2025/9jd9_61385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jd9_61385/09_2025/9jd9_61385.map" model { file = "/net/cci-nas-00/data/ceres_data/9jd9_61385/09_2025/9jd9_61385_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jd9_61385/09_2025/9jd9_61385_neut.cif" } resolution = 3.05 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= 0.060 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ARG:plan': 2, 'TYR:plan': 1} 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: 1.25, per 1000 atoms: 0.28 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: 0.55 Conformation dependent library (CDL) restraints added in 190.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.09 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: 0.60 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.900 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.770 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (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 ARG 0.002 0.000 ARG A 583 TYR 0.015 0.001 TYR A 137 PHE 0.020 0.001 PHE A 58 TRP 0.010 0.001 TRP A 113 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 4653) covalent geometry : angle 0.61515 ( 6291) SS BOND : bond 0.00141 ( 1) SS BOND : angle 1.58395 ( 2) hydrogen bonds : bond 0.21745 ( 281) hydrogen bonds : angle 7.76372 ( 828) Misc. bond : bond 0.68259 ( 1) link_NAG-ASN : bond 0.04799 ( 1) link_NAG-ASN : angle 24.25370 ( 3) *********************** 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 : 0.144 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: 0.0667 time to fit residues: 5.9592 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 : 0.161 ------------------------------------------------------------------------------- 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 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.118195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.089461 restraints weight = 5571.652| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.01 r_work: 0.2764 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1241 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= 0.142 Angle : 0.580 9.159 6296 Z= 0.293 Chirality : 0.040 0.146 684 Planarity : 0.005 0.041 754 Dihedral : 7.153 50.312 711 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.93 % Allowed : 4.71 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.35), residues: 548 helix: 1.03 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.88 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.024 0.002 TYR A 137 PHE 0.018 0.001 PHE A 58 TRP 0.018 0.001 TRP A 470 HIS 0.006 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4653) covalent geometry : angle 0.56809 ( 6291) SS BOND : bond 0.00702 ( 1) SS BOND : angle 3.38129 ( 2) hydrogen bonds : bond 0.04795 ( 281) hydrogen bonds : angle 5.01393 ( 828) Misc. bond : bond 0.00052 ( 1) link_NAG-ASN : bond 0.00370 ( 1) link_NAG-ASN : angle 4.55093 ( 3) *********************** 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 70 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.180 Fit side-chains REVERT: A 107 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 179 ASN cc_start: 0.6232 (t0) cc_final: 0.5956 (t0) REVERT: A 202 ASN cc_start: 0.8478 (t0) cc_final: 0.8184 (t0) REVERT: A 587 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7214 (ttp-110) outliers start: 9 outliers final: 8 residues processed: 66 average time/residue: 0.0591 time to fit residues: 5.4058 Evaluate side-chains 66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.117336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.088636 restraints weight = 5602.357| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.06 r_work: 0.2746 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1544 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= 0.146 Angle : 0.544 9.678 6296 Z= 0.271 Chirality : 0.040 0.145 684 Planarity : 0.004 0.041 754 Dihedral : 7.082 55.239 711 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.36 % Allowed : 7.92 % Favored : 89.72 % 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 aren not related in a simple way. whole: 0.58 (0.35), residues: 548 helix: 1.28 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.86 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.026 0.002 TYR A 137 PHE 0.013 0.001 PHE A 58 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4653) covalent geometry : angle 0.53632 ( 6291) SS BOND : bond 0.00593 ( 1) SS BOND : angle 2.72550 ( 2) hydrogen bonds : bond 0.04222 ( 281) hydrogen bonds : angle 4.70632 ( 828) Misc. bond : bond 0.00175 ( 1) link_NAG-ASN : bond 0.00014 ( 1) link_NAG-ASN : angle 3.66140 ( 3) *********************** 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: 11 poor density : 56 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8463 (p90) REVERT: A 179 ASN cc_start: 0.6377 (t0) cc_final: 0.6093 (t0) REVERT: A 202 ASN cc_start: 0.8517 (t0) cc_final: 0.8193 (t0) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0557 time to fit residues: 4.7349 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 : 0.177 ------------------------------------------------------------------------------- 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 282 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 0.0470 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.119797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.091354 restraints weight = 5585.283| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.02 r_work: 0.2790 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1760 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= 0.112 Angle : 0.508 9.470 6296 Z= 0.252 Chirality : 0.039 0.143 684 Planarity : 0.004 0.043 754 Dihedral : 6.746 59.509 711 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 9.85 % Favored : 88.01 % 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 aren not related in a simple way. whole: 0.83 (0.35), residues: 548 helix: 1.45 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.75 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.026 0.001 TYR A 137 PHE 0.014 0.001 PHE A 58 TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4653) covalent geometry : angle 0.50168 ( 6291) SS BOND : bond 0.00463 ( 1) SS BOND : angle 1.58565 ( 2) hydrogen bonds : bond 0.03738 ( 281) hydrogen bonds : angle 4.48312 ( 828) Misc. bond : bond 0.00143 ( 1) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 3.35410 ( 3) *********************** 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: 10 poor density : 57 time to evaluate : 0.187 Fit side-chains REVERT: A 69 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8294 (p90) REVERT: A 107 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7797 (mm-30) REVERT: A 179 ASN cc_start: 0.6242 (t0) cc_final: 0.5971 (t0) REVERT: A 202 ASN cc_start: 0.8513 (t0) cc_final: 0.8197 (t0) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.0573 time to fit residues: 4.9612 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 : 0.172 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.120315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.091807 restraints weight = 5539.867| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.01 r_work: 0.2796 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4656 Z= 0.111 Angle : 0.503 9.472 6296 Z= 0.249 Chirality : 0.038 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.558 54.871 711 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.14 % Allowed : 11.78 % Favored : 86.08 % 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 aren not related in a simple way. whole: 0.97 (0.35), residues: 548 helix: 1.56 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.73 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.025 0.001 TYR A 137 PHE 0.013 0.001 PHE A 58 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4653) covalent geometry : angle 0.49755 ( 6291) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.40086 ( 2) hydrogen bonds : bond 0.03649 ( 281) hydrogen bonds : angle 4.40514 ( 828) Misc. bond : bond 0.00118 ( 1) link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 3.35084 ( 3) *********************** 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: 10 poor density : 58 time to evaluate : 0.180 Fit side-chains REVERT: A 69 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8128 (p90) REVERT: A 107 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 179 ASN cc_start: 0.6276 (t0) cc_final: 0.6005 (t0) REVERT: A 202 ASN cc_start: 0.8517 (t0) cc_final: 0.8195 (t0) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.0550 time to fit residues: 4.9670 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 : 0.211 ------------------------------------------------------------------------------- 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 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.0010 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 0.0070 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.2582 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.132895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.106423 restraints weight = 5563.339| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.92 r_work: 0.2880 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4656 Z= 0.095 Angle : 0.486 9.391 6296 Z= 0.240 Chirality : 0.038 0.143 684 Planarity : 0.004 0.043 754 Dihedral : 6.284 55.969 711 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.93 % Allowed : 11.99 % Favored : 86.08 % 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 aren not related in a simple way. whole: 1.13 (0.35), residues: 548 helix: 1.70 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.73 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.023 0.001 TYR A 137 PHE 0.011 0.001 PHE A 58 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 4653) covalent geometry : angle 0.48057 ( 6291) SS BOND : bond 0.00325 ( 1) SS BOND : angle 1.12154 ( 2) hydrogen bonds : bond 0.03408 ( 281) hydrogen bonds : angle 4.27017 ( 828) Misc. bond : bond 0.00104 ( 1) link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 3.36982 ( 3) *********************** 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 69 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7733 (p90) REVERT: A 179 ASN cc_start: 0.6319 (t0) cc_final: 0.6016 (t0) REVERT: A 202 ASN cc_start: 0.8402 (t0) cc_final: 0.8088 (t0) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.0573 time to fit residues: 5.2376 Evaluate side-chains 63 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.121591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.092936 restraints weight = 5545.886| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.05 r_work: 0.2771 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1935 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= 0.139 Angle : 0.516 9.469 6296 Z= 0.256 Chirality : 0.039 0.145 684 Planarity : 0.004 0.043 754 Dihedral : 6.540 58.330 711 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.14 % Allowed : 11.78 % Favored : 86.08 % 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 aren not related in a simple way. whole: 1.07 (0.36), residues: 548 helix: 1.64 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.70 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.024 0.001 TYR A 69 PHE 0.017 0.001 PHE A 58 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4653) covalent geometry : angle 0.51024 ( 6291) SS BOND : bond 0.00264 ( 1) SS BOND : angle 1.78011 ( 2) hydrogen bonds : bond 0.03735 ( 281) hydrogen bonds : angle 4.40888 ( 828) Misc. bond : bond 0.00110 ( 1) link_NAG-ASN : bond 0.00038 ( 1) link_NAG-ASN : angle 3.35023 ( 3) *********************** 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 68 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.176 Fit side-chains REVERT: A 179 ASN cc_start: 0.6445 (t0) cc_final: 0.6150 (t0) REVERT: A 202 ASN cc_start: 0.8560 (t0) cc_final: 0.8222 (t0) outliers start: 10 outliers final: 10 residues processed: 64 average time/residue: 0.0553 time to fit residues: 4.9098 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 : 0.188 ------------------------------------------------------------------------------- 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 282 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.127580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.100917 restraints weight = 5553.599| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.86 r_work: 0.2851 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1973 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= 0.133 Angle : 0.512 9.445 6296 Z= 0.254 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.595 59.983 711 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 12.42 % 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 aren not related in a simple way. whole: 1.06 (0.35), residues: 548 helix: 1.64 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.021 0.001 TYR A 69 PHE 0.016 0.001 PHE A 58 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4653) covalent geometry : angle 0.50603 ( 6291) SS BOND : bond 0.00319 ( 1) SS BOND : angle 1.60992 ( 2) hydrogen bonds : bond 0.03701 ( 281) hydrogen bonds : angle 4.40863 ( 828) Misc. bond : bond 0.00111 ( 1) link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 3.33797 ( 3) *********************** 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: 9 poor density : 56 time to evaluate : 0.176 Fit side-chains REVERT: A 69 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7894 (p90) REVERT: A 179 ASN cc_start: 0.6483 (t0) cc_final: 0.6195 (t0) REVERT: A 202 ASN cc_start: 0.8496 (t0) cc_final: 0.8144 (t0) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.0579 time to fit residues: 5.0432 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 : 0.164 ------------------------------------------------------------------------------- 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 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.123194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094291 restraints weight = 5512.640| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.06 r_work: 0.2786 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2035 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= 0.115 Angle : 0.507 9.432 6296 Z= 0.251 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.504 59.594 711 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.57 % Allowed : 12.21 % 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 aren not related in a simple way. whole: 1.13 (0.35), residues: 548 helix: 1.70 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.019 0.001 TYR A 137 PHE 0.014 0.001 PHE A 58 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4653) covalent geometry : angle 0.50113 ( 6291) SS BOND : bond 0.00338 ( 1) SS BOND : angle 1.40858 ( 2) hydrogen bonds : bond 0.03604 ( 281) hydrogen bonds : angle 4.40078 ( 828) Misc. bond : bond 0.00108 ( 1) link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 3.33307 ( 3) *********************** 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 68 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.180 Fit side-chains REVERT: A 69 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7926 (p90) REVERT: A 107 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 179 ASN cc_start: 0.6527 (t0) cc_final: 0.6243 (t0) REVERT: A 202 ASN cc_start: 0.8527 (t0) cc_final: 0.8204 (t0) REVERT: A 442 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8246 (tp) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.0540 time to fit residues: 4.8537 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 : 0.166 ------------------------------------------------------------------------------- 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 442 LEU 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 23 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.128165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.102757 restraints weight = 5485.990| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.78 r_work: 0.2938 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1990 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= 0.142 Angle : 0.523 9.461 6296 Z= 0.261 Chirality : 0.039 0.145 684 Planarity : 0.004 0.044 754 Dihedral : 6.667 57.339 711 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 13.06 % Favored : 85.01 % 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 aren not related in a simple way. whole: 1.06 (0.35), residues: 548 helix: 1.63 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.70 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.024 0.001 TYR A 69 PHE 0.018 0.001 PHE A 58 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4653) covalent geometry : angle 0.51754 ( 6291) SS BOND : bond 0.00300 ( 1) SS BOND : angle 1.79330 ( 2) hydrogen bonds : bond 0.03783 ( 281) hydrogen bonds : angle 4.46170 ( 828) Misc. bond : bond 0.00114 ( 1) link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 3.35342 ( 3) ********************** 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 : 0.167 Fit side-chains REVERT: A 107 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7796 (tt0) REVERT: A 179 ASN cc_start: 0.6731 (t0) cc_final: 0.6481 (t0) REVERT: A 202 ASN cc_start: 0.8604 (t0) cc_final: 0.8307 (t0) outliers start: 9 outliers final: 9 residues processed: 61 average time/residue: 0.0569 time to fit residues: 4.8406 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 : 0.142 ------------------------------------------------------------------------------- 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 39 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.128845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102329 restraints weight = 5486.872| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.87 r_work: 0.2871 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2024 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= 0.134 Angle : 0.516 9.447 6296 Z= 0.256 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.680 55.867 711 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.14 % Allowed : 12.85 % Favored : 85.01 % 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 aren not related in a simple way. whole: 1.09 (0.36), residues: 548 helix: 1.65 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.69 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.021 0.001 TYR A 69 PHE 0.016 0.001 PHE A 58 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4653) covalent geometry : angle 0.51028 ( 6291) SS BOND : bond 0.00331 ( 1) SS BOND : angle 1.59287 ( 2) hydrogen bonds : bond 0.03713 ( 281) hydrogen bonds : angle 4.42939 ( 828) Misc. bond : bond 0.00113 ( 1) link_NAG-ASN : bond 0.00022 ( 1) link_NAG-ASN : angle 3.33345 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1336.49 seconds wall clock time: 23 minutes 34.63 seconds (1414.63 seconds total)