Starting phenix.real_space_refine on Thu Jul 2 05:50:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7odf_12827/07_2026/7odf_12827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7odf_12827/07_2026/7odf_12827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7odf_12827/07_2026/7odf_12827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7odf_12827/07_2026/7odf_12827.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7odf_12827/07_2026/7odf_12827.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7odf_12827/07_2026/7odf_12827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7odf_12827/07_2026/7odf_12827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7odf_12827/07_2026/7odf_12827.map" } resolution = 2.66 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= 1.000 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: 7 Type Number sf(0) Gaussians Ni 1 6.56 5 Zn 1 6.06 5 P 78 5.49 5 S 16 5.16 5 C 4068 2.51 5 N 1216 2.21 5 O 1467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6847 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5205 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 30, 'TRANS': 672} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 4, 'GLU:plan': 26, 'ARG:plan': 7, 'ASN:plan1': 15, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 256 Chain: "E" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Classifications: {'DNA': 2} Link IDs: {'rna3p': 1} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 919 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 36} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' NI': 1, ' ZN': 1} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4879 SG CYS A 680 72.409 39.562 72.141 1.00106.49 S ATOM 4900 SG CYS A 683 76.785 37.518 72.841 1.00112.67 S ATOM 5015 SG CYS A 701 74.842 39.676 74.908 1.00117.90 S Time building chain proxies: 1.30, per 1000 atoms: 0.19 Number of scatterers: 6847 At special positions: 0 Unit cell: (84.864, 98.176, 115.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ni 1 28.00 S 16 16.00 P 78 15.00 O 1467 8.00 N 1216 7.00 C 4068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 269.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 701 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 683 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 680 " 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 50.2% alpha, 8.1% beta 29 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 removed outlier: 3.779A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 35 removed outlier: 3.631A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 47 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.571A pdb=" N SER A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 121 through 160 removed outlier: 3.593A pdb=" N THR A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.618A pdb=" N GLU A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 445 through 473 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 501 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.529A pdb=" N SER A 512 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 513 " --> pdb=" O TRP A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 548 through 556 Processing helix chain 'A' and resid 561 through 579 Processing helix chain 'A' and resid 580 through 608 removed outlier: 3.795A pdb=" N LYS A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.588A pdb=" N PHE A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 710 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.238A pdb=" N ASN A 61 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 330 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 65 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP A 328 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 442 removed outlier: 3.538A pdb=" N VAL A 407 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA A 408 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 616 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 410 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLU A 618 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N VAL A 412 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS A 667 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 537 through 538 Processing sheet with id=AA4, first strand: chain 'A' and resid 695 through 697 269 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1905 1.34 - 1.46: 1707 1.46 - 1.58: 3356 1.58 - 1.70: 152 1.70 - 1.82: 22 Bond restraints: 7142 Sorted by residual: bond pdb=" C3' DT E 22 " pdb=" C2' DT E 22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.66e+00 bond pdb=" C3' DC E 14 " pdb=" C2' DC E 14 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.93e+00 bond pdb=" O4' DC E 14 " pdb=" C1' DC E 14 " ideal model delta sigma weight residual 1.420 1.396 0.024 1.10e-02 8.26e+03 4.63e+00 bond pdb=" C1' DC E 6 " pdb=" N1 DC E 6 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.49e+00 bond pdb=" C3' DA E 20 " pdb=" O3' DA E 20 " ideal model delta sigma weight residual 1.435 1.408 0.027 1.30e-02 5.92e+03 4.41e+00 ... (remaining 7137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 9676 1.27 - 2.53: 318 2.53 - 3.80: 50 3.80 - 5.06: 8 5.06 - 6.33: 4 Bond angle restraints: 10056 Sorted by residual: angle pdb=" N3 DT G 6 " pdb=" C4 DT G 6 " pdb=" O4 DT G 6 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT E 18 " pdb=" C4 DT E 18 " pdb=" O4 DT E 18 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E 22 " pdb=" C4 DT E 22 " pdb=" O4 DT E 22 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT G 2 " pdb=" C4 DT G 2 " pdb=" O4 DT G 2 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT G 5 " pdb=" C4 DT G 5 " pdb=" O4 DT G 5 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 10051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 3899 34.02 - 68.03: 157 68.03 - 102.05: 7 102.05 - 136.06: 2 136.06 - 170.08: 2 Dihedral angle restraints: 4067 sinusoidal: 2019 harmonic: 2048 Sorted by residual: dihedral pdb=" O4' U F 3 " pdb=" C1' U F 3 " pdb=" N1 U F 3 " pdb=" C2 U F 3 " ideal model delta sinusoidal sigma weight residual 200.00 29.92 170.08 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U F 44 " pdb=" C1' U F 44 " pdb=" N1 U F 44 " pdb=" C2 U F 44 " ideal model delta sinusoidal sigma weight residual -160.00 -103.50 -56.50 1 1.50e+01 4.44e-03 1.91e+01 dihedral pdb=" C4' DT E 11 " pdb=" C3' DT E 11 " pdb=" O3' DT E 11 " pdb=" P DA E 12 " ideal model delta sinusoidal sigma weight residual 220.00 79.58 140.42 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 4064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 769 0.031 - 0.062: 278 0.062 - 0.092: 83 0.092 - 0.123: 47 0.123 - 0.154: 8 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA GLU A 591 " pdb=" N GLU A 591 " pdb=" C GLU A 591 " pdb=" CB GLU A 591 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA LYS A 625 " pdb=" N LYS A 625 " pdb=" C LYS A 625 " pdb=" CB LYS A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 193 " pdb=" N ILE A 193 " pdb=" C ILE A 193 " pdb=" CB ILE A 193 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1182 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 587 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C LYS A 587 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A 587 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 588 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 218 " 0.013 2.00e-02 2.50e+03 1.44e-02 4.13e+00 pdb=" CG TYR A 218 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 218 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 218 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 218 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 218 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 218 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 218 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 337 " -0.016 2.00e-02 2.50e+03 1.24e-02 3.09e+00 pdb=" CG TYR A 337 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 337 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 337 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 337 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 337 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 337 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 337 " 0.001 2.00e-02 2.50e+03 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 32 2.54 - 3.13: 5116 3.13 - 3.72: 11540 3.72 - 4.31: 16290 4.31 - 4.90: 25151 Nonbonded interactions: 58129 Sorted by model distance: nonbonded pdb=" OD1 ASP A 413 " pdb="NI NI A 801 " model vdw 1.952 2.180 nonbonded pdb=" OG1 THR A 60 " pdb=" O VAL A 372 " model vdw 2.198 3.040 nonbonded pdb=" O ASN A 275 " pdb=" O2' G F 14 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 296 " pdb=" OP2 C F 19 " model vdw 2.239 3.040 nonbonded pdb=" O LYS A 400 " pdb=" OG SER A 403 " model vdw 2.336 3.040 ... (remaining 58124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.840 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:4.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.009 0.661 7145 Z= 0.373 Angle : 0.539 6.331 10056 Z= 0.385 Chirality : 0.040 0.154 1185 Planarity : 0.003 0.032 1014 Dihedral : 16.741 170.081 2743 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.32), residues: 699 helix: 2.00 (0.29), residues: 315 sheet: 0.19 (0.61), residues: 70 loop : 0.20 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.033 0.002 TYR A 218 PHE 0.020 0.001 PHE A 341 TRP 0.010 0.001 TRP A 636 HIS 0.002 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.27 ( 7142) covalent geometry : angle 0.53923 / 0.38 (10056) hydrogen bonds : bond 0.19328 / 13.18 ( 339) hydrogen bonds : angle 6.99053 / 5.12 ( 892) metal coordination : bond 0.38155 / 20.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.164 Fit side-chains REVERT: A 621 ASP cc_start: 0.7918 (t70) cc_final: 0.7329 (t70) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3951 time to fit residues: 30.9907 Evaluate side-chains 46 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105693 restraints weight = 9022.252| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.02 r_work: 0.3207 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7145 Z= 0.193 Angle : 0.575 7.093 10056 Z= 0.312 Chirality : 0.042 0.170 1185 Planarity : 0.004 0.032 1014 Dihedral : 17.395 170.633 1653 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.57 % Allowed : 6.85 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.32), residues: 699 helix: 2.26 (0.29), residues: 312 sheet: -0.32 (0.58), residues: 82 loop : 0.25 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 343 TYR 0.022 0.002 TYR A 218 PHE 0.022 0.001 PHE A 488 TRP 0.013 0.001 TRP A 636 HIS 0.005 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 ( 7142) covalent geometry : angle 0.57482 / 0.31 (10056) hydrogen bonds : bond 0.04971 / 3.38 ( 339) hydrogen bonds : angle 4.64534 / 3.57 ( 892) metal coordination : bond 0.01652 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.173 Fit side-chains REVERT: A 391 ARG cc_start: 0.8589 (ptp-170) cc_final: 0.8356 (ptp-170) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.3776 time to fit residues: 22.5440 Evaluate side-chains 49 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 726 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 35 optimal weight: 0.0770 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.0170 chunk 5 optimal weight: 0.8980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109010 restraints weight = 9511.123| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.14 r_work: 0.3298 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7145 Z= 0.124 Angle : 0.499 5.729 10056 Z= 0.274 Chirality : 0.039 0.167 1185 Planarity : 0.003 0.031 1014 Dihedral : 17.264 169.977 1653 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.17 % Allowed : 9.39 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.32), residues: 699 helix: 2.42 (0.29), residues: 312 sheet: -0.43 (0.58), residues: 82 loop : 0.31 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.024 0.001 TYR A 218 PHE 0.019 0.001 PHE A 488 TRP 0.012 0.001 TRP A 636 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 7142) covalent geometry : angle 0.49949 / 0.27 (10056) hydrogen bonds : bond 0.04033 / 2.70 ( 339) hydrogen bonds : angle 4.14837 / 3.17 ( 892) metal coordination : bond 0.00803 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 621 ASP cc_start: 0.8117 (t70) cc_final: 0.7383 (t70) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.3533 time to fit residues: 23.0801 Evaluate side-chains 52 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 726 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106535 restraints weight = 9504.334| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.14 r_work: 0.3261 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7145 Z= 0.159 Angle : 0.506 6.729 10056 Z= 0.277 Chirality : 0.040 0.161 1185 Planarity : 0.003 0.035 1014 Dihedral : 17.270 171.014 1653 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.57 % Allowed : 11.15 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.32), residues: 699 helix: 2.28 (0.29), residues: 316 sheet: -0.46 (0.58), residues: 82 loop : 0.34 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.025 0.001 TYR A 218 PHE 0.010 0.001 PHE A 488 TRP 0.010 0.001 TRP A 636 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 7142) covalent geometry : angle 0.50623 / 0.28 (10056) hydrogen bonds : bond 0.03889 / 2.61 ( 339) hydrogen bonds : angle 4.10736 / 3.13 ( 892) metal coordination : bond 0.00155 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 621 ASP cc_start: 0.8128 (t70) cc_final: 0.7453 (t70) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.3667 time to fit residues: 21.2008 Evaluate side-chains 54 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.0170 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107316 restraints weight = 9522.307| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.13 r_work: 0.3280 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7145 Z= 0.134 Angle : 0.488 6.426 10056 Z= 0.267 Chirality : 0.039 0.147 1185 Planarity : 0.003 0.032 1014 Dihedral : 17.282 171.010 1653 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.74 % Allowed : 10.37 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.32), residues: 699 helix: 2.37 (0.29), residues: 316 sheet: -0.50 (0.58), residues: 82 loop : 0.35 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.023 0.001 TYR A 218 PHE 0.010 0.001 PHE A 640 TRP 0.011 0.001 TRP A 636 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 7142) covalent geometry : angle 0.48751 / 0.27 (10056) hydrogen bonds : bond 0.03609 / 2.42 ( 339) hydrogen bonds : angle 3.99659 / 3.05 ( 892) metal coordination : bond 0.00144 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7965 (tp) REVERT: A 621 ASP cc_start: 0.8152 (t70) cc_final: 0.7486 (t70) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.2879 time to fit residues: 19.9780 Evaluate side-chains 60 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 726 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102628 restraints weight = 9661.568| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.08 r_work: 0.3262 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7145 Z= 0.339 Angle : 0.623 5.974 10056 Z= 0.339 Chirality : 0.046 0.187 1185 Planarity : 0.004 0.029 1014 Dihedral : 17.723 174.742 1653 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.74 % Allowed : 11.94 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.32), residues: 699 helix: 2.14 (0.29), residues: 313 sheet: -0.16 (0.64), residues: 74 loop : 0.23 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.031 0.003 TYR A 218 PHE 0.013 0.002 PHE A 281 TRP 0.015 0.002 TRP A 72 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.34 ( 7142) covalent geometry : angle 0.62320 / 0.34 (10056) hydrogen bonds : bond 0.05040 / 3.40 ( 339) hydrogen bonds : angle 4.31565 / 3.27 ( 892) metal coordination : bond 0.00336 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 621 ASP cc_start: 0.8318 (t70) cc_final: 0.7693 (t70) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 0.3634 time to fit residues: 23.0571 Evaluate side-chains 59 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 48 optimal weight: 9.9990 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.105286 restraints weight = 9366.259| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.12 r_work: 0.3241 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7145 Z= 0.130 Angle : 0.511 7.642 10056 Z= 0.276 Chirality : 0.040 0.167 1185 Planarity : 0.003 0.030 1014 Dihedral : 17.608 172.197 1653 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.54 % Allowed : 12.92 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.32), residues: 699 helix: 2.29 (0.29), residues: 316 sheet: -0.32 (0.61), residues: 74 loop : 0.33 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 691 TYR 0.024 0.001 TYR A 218 PHE 0.011 0.001 PHE A 640 TRP 0.012 0.001 TRP A 636 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 7142) covalent geometry : angle 0.51091 / 0.28 (10056) hydrogen bonds : bond 0.03644 / 2.44 ( 339) hydrogen bonds : angle 4.08387 / 3.12 ( 892) metal coordination : bond 0.00137 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8017 (tp) outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.3401 time to fit residues: 22.3805 Evaluate side-chains 55 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 0.0070 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 567 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109513 restraints weight = 9724.519| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.03 r_work: 0.3334 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7145 Z= 0.133 Angle : 0.496 7.978 10056 Z= 0.270 Chirality : 0.039 0.150 1185 Planarity : 0.003 0.030 1014 Dihedral : 17.451 172.234 1653 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.35 % Allowed : 14.09 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.32), residues: 699 helix: 2.39 (0.29), residues: 316 sheet: -0.56 (0.58), residues: 80 loop : 0.29 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 691 TYR 0.030 0.001 TYR A 218 PHE 0.010 0.001 PHE A 640 TRP 0.011 0.001 TRP A 636 HIS 0.002 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 7142) covalent geometry : angle 0.49564 / 0.27 (10056) hydrogen bonds : bond 0.03545 / 2.36 ( 339) hydrogen bonds : angle 3.96315 / 3.03 ( 892) metal coordination : bond 0.00208 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 391 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8293 (ptp-170) REVERT: A 610 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8061 (tp) REVERT: A 621 ASP cc_start: 0.8223 (t70) cc_final: 0.7554 (t70) outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.3170 time to fit residues: 19.1100 Evaluate side-chains 54 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.0030 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.106494 restraints weight = 9553.555| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.01 r_work: 0.3333 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7145 Z= 0.164 Angle : 0.509 9.158 10056 Z= 0.275 Chirality : 0.039 0.151 1185 Planarity : 0.003 0.030 1014 Dihedral : 17.455 172.942 1653 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.96 % Allowed : 14.87 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.32), residues: 699 helix: 2.38 (0.29), residues: 316 sheet: -0.21 (0.62), residues: 72 loop : 0.38 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.032 0.002 TYR A 218 PHE 0.014 0.001 PHE A 341 TRP 0.011 0.001 TRP A 636 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 7142) covalent geometry : angle 0.50881 / 0.27 (10056) hydrogen bonds : bond 0.03634 / 2.43 ( 339) hydrogen bonds : angle 3.99977 / 3.06 ( 892) metal coordination : bond 0.00134 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8101 (tp) REVERT: A 621 ASP cc_start: 0.8252 (t70) cc_final: 0.7597 (t70) outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 0.3618 time to fit residues: 20.9652 Evaluate side-chains 55 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN A 478 GLN A 567 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104313 restraints weight = 9612.447| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.03 r_work: 0.3299 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7145 Z= 0.221 Angle : 0.543 7.397 10056 Z= 0.295 Chirality : 0.041 0.163 1185 Planarity : 0.003 0.029 1014 Dihedral : 17.537 174.463 1653 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.96 % Allowed : 14.68 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.32), residues: 699 helix: 2.29 (0.29), residues: 315 sheet: -0.22 (0.62), residues: 74 loop : 0.34 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.037 0.002 TYR A 218 PHE 0.016 0.002 PHE A 341 TRP 0.012 0.001 TRP A 675 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 ( 7142) covalent geometry : angle 0.54345 / 0.30 (10056) hydrogen bonds : bond 0.04023 / 2.69 ( 339) hydrogen bonds : angle 4.08325 / 3.12 ( 892) metal coordination : bond 0.00187 / 0.09 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8148 (tp) REVERT: A 621 ASP cc_start: 0.8270 (t70) cc_final: 0.7610 (t70) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.3254 time to fit residues: 18.2480 Evaluate side-chains 52 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103002 restraints weight = 9455.940| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.13 r_work: 0.3210 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7145 Z= 0.204 Angle : 0.548 8.842 10056 Z= 0.293 Chirality : 0.041 0.167 1185 Planarity : 0.003 0.029 1014 Dihedral : 17.562 174.670 1653 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.96 % Allowed : 14.87 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.32), residues: 699 helix: 2.26 (0.29), residues: 315 sheet: -0.43 (0.59), residues: 78 loop : 0.39 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.037 0.002 TYR A 218 PHE 0.016 0.001 PHE A 341 TRP 0.014 0.001 TRP A 675 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 ( 7142) covalent geometry : angle 0.54826 / 0.29 (10056) hydrogen bonds : bond 0.03877 / 2.60 ( 339) hydrogen bonds : angle 4.06371 / 3.11 ( 892) metal coordination : bond 0.00147 / 0.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.87 seconds wall clock time: 36 minutes 53.86 seconds (2213.86 seconds total)