Starting phenix.real_space_refine on Sat Aug 23 05:32:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fgx_29077/08_2025/8fgx_29077_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fgx_29077/08_2025/8fgx_29077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fgx_29077/08_2025/8fgx_29077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fgx_29077/08_2025/8fgx_29077.map" model { file = "/net/cci-nas-00/data/ceres_data/8fgx_29077/08_2025/8fgx_29077_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fgx_29077/08_2025/8fgx_29077_trim.cif" } resolution = 2.62 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= 0.000 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: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 3186 2.51 5 N 838 2.21 5 O 980 1.98 5 H 4873 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9899 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3252 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3190 Classifications: {'peptide': 216} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3415 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.21, per 1000 atoms: 0.22 Number of scatterers: 9899 At special positions: 0 Unit cell: (106.683, 99.24, 83.527, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 980 8.00 N 838 7.00 C 3186 6.00 H 4873 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 419 " - pdb=" SG CYS C 435 " distance=2.03 Simple disulfide: pdb=" SG CYS C 517 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 548 " - pdb=" SG CYS C 563 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 701 " - " ASN C 396 " " NAG C 702 " - " ASN C 453 " " NAG C 703 " - " ASN C 494 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 191.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 11.3% alpha, 46.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.701A pdb=" N PHE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.686A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.727A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 506 through 511 removed outlier: 3.812A pdb=" N THR C 510 " --> pdb=" O LYS C 507 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 511 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 4.006A pdb=" N LYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 626 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR A 49 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 118 removed outlier: 4.963A pdb=" N SER A 131 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 181 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL A 133 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 179 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU A 135 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 177 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN A 137 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 175 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.415A pdb=" N MET B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.684A pdb=" N CYS B 96 " --> pdb=" O TRP B 111 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP B 111 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY B 98 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.061A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.061A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.313A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.903A pdb=" N VAL C 410 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS C 417 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 486 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE C 469 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS C 488 " --> pdb=" O LYS C 467 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 466 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP C 445 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.727A pdb=" N THR C 520 " --> pdb=" O PRO C 581 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 582 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS C 563 " --> pdb=" O VAL C 543 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 486 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: 2.36 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4858 1.03 - 1.23: 18 1.23 - 1.42: 2174 1.42 - 1.61: 2942 1.61 - 1.81: 29 Bond restraints: 10021 Sorted by residual: bond pdb=" N ILE C 391 " pdb=" CA ILE C 391 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 bond pdb=" N ILE C 391 " pdb=" H ILE C 391 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C1 NAG C 703 " pdb=" O5 NAG C 703 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 10016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 16789 0.92 - 1.84: 1181 1.84 - 2.76: 45 2.76 - 3.68: 25 3.68 - 4.60: 3 Bond angle restraints: 18043 Sorted by residual: angle pdb=" CA PRO C 608 " pdb=" C PRO C 608 " pdb=" N GLY C 609 " ideal model delta sigma weight residual 114.66 116.82 -2.16 1.34e+00 5.57e-01 2.60e+00 angle pdb=" CA ILE C 391 " pdb=" N ILE C 391 " pdb=" H ILE C 391 " ideal model delta sigma weight residual 114.00 109.40 4.60 3.00e+00 1.11e-01 2.35e+00 angle pdb=" N ALA A 51 " pdb=" CA ALA A 51 " pdb=" C ALA A 51 " ideal model delta sigma weight residual 110.80 114.05 -3.25 2.13e+00 2.20e-01 2.33e+00 angle pdb=" N SER C 597 " pdb=" CA SER C 597 " pdb=" C SER C 597 " ideal model delta sigma weight residual 113.18 111.31 1.87 1.33e+00 5.65e-01 1.98e+00 angle pdb=" C TYR A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 121.54 124.17 -2.63 1.91e+00 2.74e-01 1.90e+00 ... (remaining 18038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4525 17.41 - 34.81: 173 34.81 - 52.22: 88 52.22 - 69.62: 40 69.62 - 87.03: 15 Dihedral angle restraints: 4841 sinusoidal: 2631 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ARG A 142 " pdb=" C ARG A 142 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA PHE B 95 " pdb=" C PHE B 95 " pdb=" N CYS B 96 " pdb=" CA CYS B 96 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 68.07 24.93 1 1.00e+01 1.00e-02 8.94e+00 ... (remaining 4838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 504 0.033 - 0.065: 187 0.065 - 0.097: 37 0.097 - 0.130: 58 0.130 - 0.162: 2 Chirality restraints: 788 Sorted by residual: chirality pdb=" C1 NAG C 703 " pdb=" ND2 ASN C 494 " pdb=" C2 NAG C 703 " pdb=" O5 NAG C 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE C 531 " pdb=" N ILE C 531 " pdb=" C ILE C 531 " pdb=" CB ILE C 531 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE A 21 " pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CB ILE A 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 785 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 607 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 608 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 608 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 608 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " -0.022 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 157 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 209 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO B 210 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.014 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 849 2.22 - 2.82: 21627 2.82 - 3.41: 25899 3.41 - 4.01: 38020 4.01 - 4.60: 56223 Nonbonded interactions: 142618 Sorted by model distance: nonbonded pdb=" OE1 GLU A 123 " pdb=" H GLU A 123 " model vdw 1.630 2.450 nonbonded pdb=" HH TYR A 36 " pdb=" OE1 GLN A 89 " model vdw 1.633 2.450 nonbonded pdb=" O ASP A 82 " pdb=" HH TYR A 86 " model vdw 1.648 2.450 nonbonded pdb="HE22 GLN B 6 " pdb=" O TYR B 94 " model vdw 1.665 2.450 nonbonded pdb=" OE1 GLN C 409 " pdb="HE21 GLN C 415 " model vdw 1.671 2.450 ... (remaining 142613 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: 2.910 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: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.360 Find NCS groups from input model: 0.040 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 : 0.003 0.031 5158 Z= 0.131 Angle : 0.451 4.136 7025 Z= 0.231 Chirality : 0.044 0.162 788 Planarity : 0.003 0.041 883 Dihedral : 9.989 87.028 1879 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.41 (0.36), residues: 631 helix: -0.33 (0.92), residues: 33 sheet: 0.66 (0.31), residues: 270 loop : 1.58 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.006 0.001 TYR A 91 PHE 0.010 0.001 PHE A 46 TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5148) covalent geometry : angle 0.44566 ( 7002) SS BOND : bond 0.00362 ( 7) SS BOND : angle 0.60592 ( 14) hydrogen bonds : bond 0.19990 ( 184) hydrogen bonds : angle 9.49526 ( 486) link_NAG-ASN : bond 0.00152 ( 3) link_NAG-ASN : angle 1.97246 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.7999 time to fit residues: 107.5874 Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.039071 restraints weight = 47776.368| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.28 r_work: 0.2558 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5158 Z= 0.139 Angle : 0.509 4.641 7025 Z= 0.272 Chirality : 0.045 0.154 788 Planarity : 0.004 0.038 883 Dihedral : 5.189 41.516 745 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.18 % Allowed : 6.12 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.27 (0.35), residues: 631 helix: -0.25 (0.82), residues: 33 sheet: 0.62 (0.30), residues: 276 loop : 1.42 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 218 TYR 0.007 0.001 TYR A 49 PHE 0.012 0.001 PHE B 95 TRP 0.008 0.001 TRP C 428 HIS 0.003 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5148) covalent geometry : angle 0.50535 ( 7002) SS BOND : bond 0.00266 ( 7) SS BOND : angle 0.74902 ( 14) hydrogen bonds : bond 0.03861 ( 184) hydrogen bonds : angle 6.32898 ( 486) link_NAG-ASN : bond 0.00191 ( 3) link_NAG-ASN : angle 1.54735 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9210 (tt0) cc_final: 0.8885 (tt0) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 1.5649 time to fit residues: 72.9282 Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 = 0.3090 r_free = 0.3090 target = 0.051216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.038253 restraints weight = 48396.833| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.22 r_work: 0.2539 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5158 Z= 0.163 Angle : 0.495 4.569 7025 Z= 0.263 Chirality : 0.045 0.146 788 Planarity : 0.004 0.034 883 Dihedral : 4.790 35.113 745 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.36 % Allowed : 6.12 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.23 (0.34), residues: 631 helix: -0.24 (0.82), residues: 34 sheet: 0.64 (0.30), residues: 274 loop : 1.35 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 416 TYR 0.007 0.001 TYR A 49 PHE 0.010 0.001 PHE B 95 TRP 0.007 0.001 TRP C 428 HIS 0.002 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5148) covalent geometry : angle 0.49241 ( 7002) SS BOND : bond 0.00270 ( 7) SS BOND : angle 0.69189 ( 14) hydrogen bonds : bond 0.03458 ( 184) hydrogen bonds : angle 5.79060 ( 486) link_NAG-ASN : bond 0.00154 ( 3) link_NAG-ASN : angle 1.48029 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9196 (tt0) cc_final: 0.8929 (tt0) REVERT: C 497 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8682 (mp0) outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 1.4464 time to fit residues: 58.6777 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 9 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3085 r_free = 0.3085 target = 0.050968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.037992 restraints weight = 49280.928| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.25 r_work: 0.2534 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5158 Z= 0.164 Angle : 0.493 4.468 7025 Z= 0.260 Chirality : 0.044 0.148 788 Planarity : 0.004 0.036 883 Dihedral : 4.519 29.682 745 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.21 (0.34), residues: 631 helix: -0.15 (0.86), residues: 34 sheet: 0.64 (0.29), residues: 274 loop : 1.30 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.007 0.001 TYR A 49 PHE 0.011 0.001 PHE B 95 TRP 0.006 0.001 TRP C 428 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5148) covalent geometry : angle 0.48981 ( 7002) SS BOND : bond 0.00278 ( 7) SS BOND : angle 0.69847 ( 14) hydrogen bonds : bond 0.03009 ( 184) hydrogen bonds : angle 5.48646 ( 486) link_NAG-ASN : bond 0.00142 ( 3) link_NAG-ASN : angle 1.53572 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7979 (mm-30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 1.4569 time to fit residues: 62.1033 Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.051118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.038188 restraints weight = 48657.725| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.24 r_work: 0.2543 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5158 Z= 0.127 Angle : 0.488 4.637 7025 Z= 0.256 Chirality : 0.044 0.152 788 Planarity : 0.003 0.037 883 Dihedral : 4.318 27.335 745 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.18 % Allowed : 7.19 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.24 (0.34), residues: 631 helix: -0.15 (0.87), residues: 34 sheet: 0.74 (0.30), residues: 273 loop : 1.22 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.007 0.001 TYR A 49 PHE 0.010 0.001 PHE B 95 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5148) covalent geometry : angle 0.48471 ( 7002) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.62680 ( 14) hydrogen bonds : bond 0.02723 ( 184) hydrogen bonds : angle 5.23969 ( 486) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 1.50523 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9172 (tt0) cc_final: 0.8855 (tt0) REVERT: C 623 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8347 (pp20) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 1.4068 time to fit residues: 59.7428 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 27 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 = 0.3084 r_free = 0.3084 target = 0.050808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.037911 restraints weight = 48983.601| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.24 r_work: 0.2539 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5158 Z= 0.142 Angle : 0.501 5.234 7025 Z= 0.262 Chirality : 0.044 0.152 788 Planarity : 0.003 0.038 883 Dihedral : 4.226 25.821 745 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.36 % Allowed : 7.19 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.24 (0.34), residues: 631 helix: -0.09 (0.86), residues: 34 sheet: 0.76 (0.30), residues: 273 loop : 1.21 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 142 TYR 0.007 0.001 TYR A 49 PHE 0.010 0.001 PHE B 95 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5148) covalent geometry : angle 0.49764 ( 7002) SS BOND : bond 0.00238 ( 7) SS BOND : angle 0.67261 ( 14) hydrogen bonds : bond 0.02677 ( 184) hydrogen bonds : angle 5.12824 ( 486) link_NAG-ASN : bond 0.00155 ( 3) link_NAG-ASN : angle 1.50969 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 195 GLU cc_start: 0.9167 (tt0) cc_final: 0.8871 (tt0) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 1.2074 time to fit residues: 56.4571 Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.050796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.037932 restraints weight = 48867.475| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.22 r_work: 0.2542 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5158 Z= 0.148 Angle : 0.513 5.634 7025 Z= 0.269 Chirality : 0.044 0.152 788 Planarity : 0.004 0.038 883 Dihedral : 4.157 24.491 745 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.18 % Allowed : 8.81 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.19 (0.34), residues: 631 helix: -0.38 (0.85), residues: 38 sheet: 0.76 (0.29), residues: 271 loop : 1.20 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 142 TYR 0.006 0.001 TYR A 49 PHE 0.010 0.001 PHE B 95 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5148) covalent geometry : angle 0.50947 ( 7002) SS BOND : bond 0.00229 ( 7) SS BOND : angle 0.71534 ( 14) hydrogen bonds : bond 0.02616 ( 184) hydrogen bonds : angle 5.08705 ( 486) link_NAG-ASN : bond 0.00153 ( 3) link_NAG-ASN : angle 1.51828 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 195 GLU cc_start: 0.9168 (tt0) cc_final: 0.8884 (tt0) REVERT: C 623 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8379 (pp20) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 1.2906 time to fit residues: 52.5374 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.3088 r_free = 0.3088 target = 0.050806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.037941 restraints weight = 48536.711| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.22 r_work: 0.2539 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5158 Z= 0.146 Angle : 0.527 7.435 7025 Z= 0.276 Chirality : 0.044 0.151 788 Planarity : 0.003 0.039 883 Dihedral : 4.070 23.512 745 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.22 (0.34), residues: 631 helix: -0.04 (0.87), residues: 35 sheet: 0.74 (0.30), residues: 271 loop : 1.20 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 142 TYR 0.006 0.001 TYR A 49 PHE 0.010 0.001 PHE B 95 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5148) covalent geometry : angle 0.52407 ( 7002) SS BOND : bond 0.00250 ( 7) SS BOND : angle 0.81361 ( 14) hydrogen bonds : bond 0.02573 ( 184) hydrogen bonds : angle 5.01600 ( 486) link_NAG-ASN : bond 0.00162 ( 3) link_NAG-ASN : angle 1.53041 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 195 GLU cc_start: 0.9170 (tt0) cc_final: 0.8892 (tt0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 1.1907 time to fit residues: 48.4185 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3087 r_free = 0.3087 target = 0.050704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.037763 restraints weight = 49058.838| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.24 r_work: 0.2534 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5158 Z= 0.156 Angle : 0.514 6.270 7025 Z= 0.269 Chirality : 0.044 0.153 788 Planarity : 0.003 0.039 883 Dihedral : 4.043 22.781 745 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.19 (0.34), residues: 631 helix: -0.46 (0.83), residues: 39 sheet: 0.75 (0.30), residues: 271 loop : 1.21 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 142 TYR 0.006 0.001 TYR A 49 PHE 0.010 0.001 PHE B 95 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5148) covalent geometry : angle 0.51050 ( 7002) SS BOND : bond 0.00240 ( 7) SS BOND : angle 0.76411 ( 14) hydrogen bonds : bond 0.02596 ( 184) hydrogen bonds : angle 4.99257 ( 486) link_NAG-ASN : bond 0.00149 ( 3) link_NAG-ASN : angle 1.53236 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 195 GLU cc_start: 0.9177 (tt0) cc_final: 0.8896 (tt0) REVERT: C 623 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8383 (pp20) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 1.0003 time to fit residues: 37.6999 Evaluate side-chains 36 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 0.0020 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 = 0.3085 r_free = 0.3085 target = 0.050704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.037665 restraints weight = 48795.579| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.28 r_work: 0.2527 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5158 Z= 0.164 Angle : 0.522 6.522 7025 Z= 0.273 Chirality : 0.044 0.152 788 Planarity : 0.003 0.039 883 Dihedral : 4.017 22.050 745 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.18 (0.34), residues: 631 helix: -0.45 (0.84), residues: 39 sheet: 0.74 (0.30), residues: 271 loop : 1.21 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 142 TYR 0.006 0.001 TYR A 49 PHE 0.011 0.001 PHE B 95 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5148) covalent geometry : angle 0.51834 ( 7002) SS BOND : bond 0.00253 ( 7) SS BOND : angle 0.78730 ( 14) hydrogen bonds : bond 0.02626 ( 184) hydrogen bonds : angle 4.98704 ( 486) link_NAG-ASN : bond 0.00151 ( 3) link_NAG-ASN : angle 1.56085 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9182 (tt0) cc_final: 0.8896 (tt0) REVERT: B 82 GLU cc_start: 0.8825 (tp30) cc_final: 0.8244 (tm-30) REVERT: C 623 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8400 (pp20) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 1.0245 time to fit residues: 39.5915 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 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 = 0.3091 r_free = 0.3091 target = 0.050925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.037872 restraints weight = 49059.218| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.29 r_work: 0.2533 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5158 Z= 0.140 Angle : 0.514 6.481 7025 Z= 0.268 Chirality : 0.044 0.151 788 Planarity : 0.003 0.039 883 Dihedral : 3.963 22.138 745 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.23 (0.34), residues: 631 helix: -0.34 (0.86), residues: 39 sheet: 0.79 (0.30), residues: 271 loop : 1.22 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 142 TYR 0.006 0.001 TYR A 49 PHE 0.010 0.001 PHE B 95 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5148) covalent geometry : angle 0.51067 ( 7002) SS BOND : bond 0.00217 ( 7) SS BOND : angle 0.71515 ( 14) hydrogen bonds : bond 0.02511 ( 184) hydrogen bonds : angle 4.90809 ( 486) link_NAG-ASN : bond 0.00179 ( 3) link_NAG-ASN : angle 1.53190 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.71 seconds wall clock time: 65 minutes 4.98 seconds (3904.98 seconds total)