Starting phenix.real_space_refine on Tue Aug 4 17:55:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rqm_54179/08_2026/9rqm_54179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rqm_54179/08_2026/9rqm_54179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rqm_54179/08_2026/9rqm_54179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rqm_54179/08_2026/9rqm_54179.map" model { file = "/net/cci-nas-00/data/ceres_data/9rqm_54179/08_2026/9rqm_54179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rqm_54179/08_2026/9rqm_54179.cif" } resolution = 3.06 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= 0.004 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 P 1 5.49 5 S 28 5.16 5 C 3614 2.51 5 N 911 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5532 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5344 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 654} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 143 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 18} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'IZY': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'IZY:plan-2': 1, 'IZY:plan-3': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.11, per 1000 atoms: 0.20 Number of scatterers: 5532 At special positions: 0 Unit cell: (62.6088, 88.1466, 112.861, 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 28 16.00 P 1 15.00 O 978 8.00 N 911 7.00 C 3614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 522 " - pdb=" SG CYS A 544 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 802 " - " ASN A 568 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 125.8 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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: 36 helices and 2 sheets defined 69.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 27 through 42 removed outlier: 3.873A pdb=" N ALA A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.503A pdb=" N PHE A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 118 Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.609A pdb=" N GLY A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.527A pdb=" N ILE A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 165 Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.676A pdb=" N PHE A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 189 No H-bonds generated for 'chain 'A' and resid 188 through 189' Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 193 through 212 removed outlier: 3.578A pdb=" N CYS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 215 through 229 removed outlier: 3.576A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.554A pdb=" N THR A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.752A pdb=" N ASN A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 340 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 357 through 384 removed outlier: 3.616A pdb=" N VAL A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 removed outlier: 4.004A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 Processing helix chain 'A' and resid 440 through 453 removed outlier: 4.219A pdb=" N ARG A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.819A pdb=" N THR A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 465 through 469' Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.862A pdb=" N LYS A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.588A pdb=" N VAL A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.776A pdb=" N LYS A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.804A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 606 Processing helix chain 'A' and resid 610 through 632 removed outlier: 3.537A pdb=" N ILE A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN A 632 " --> pdb=" O ILE A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 654 removed outlier: 3.891A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 678 removed outlier: 3.608A pdb=" N LEU A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 17 through 21 removed outlier: 3.812A pdb=" N GLY B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE B 21 " --> pdb=" O GLY B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 21' Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 464 removed outlier: 6.151A pdb=" N ILE A 435 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N CYS A 522 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 437 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR A 519 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS A 544 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 490 through 491 removed outlier: 6.282A pdb=" N ARG A 490 " --> pdb=" O PHE A 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 337 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.51 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: 1636 1.34 - 1.47: 1495 1.47 - 1.59: 2509 1.59 - 1.72: 1 1.72 - 1.84: 44 Bond restraints: 5685 Sorted by residual: bond pdb=" C LEU A 285 " pdb=" N LEU A 286 " ideal model delta sigma weight residual 1.335 1.393 -0.058 1.38e-02 5.25e+03 1.75e+01 bond pdb=" O26 IZY A 801 " pdb=" P27 IZY A 801 " ideal model delta sigma weight residual 1.635 1.563 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CA VAL A 77 " pdb=" CB VAL A 77 " ideal model delta sigma weight residual 1.540 1.590 -0.050 1.39e-02 5.18e+03 1.30e+01 bond pdb=" CA TRP A 581 " pdb=" C TRP A 581 " ideal model delta sigma weight residual 1.522 1.572 -0.050 1.40e-02 5.10e+03 1.25e+01 bond pdb=" O30 IZY A 801 " pdb=" P27 IZY A 801 " ideal model delta sigma weight residual 1.665 1.595 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 5680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 7002 1.43 - 2.86: 571 2.86 - 4.29: 135 4.29 - 5.73: 34 5.73 - 7.16: 6 Bond angle restraints: 7748 Sorted by residual: angle pdb=" C LEU A 653 " pdb=" CA LEU A 653 " pdb=" CB LEU A 653 " ideal model delta sigma weight residual 110.88 118.04 -7.16 1.57e+00 4.06e-01 2.08e+01 angle pdb=" C LEU A 148 " pdb=" CA LEU A 148 " pdb=" CB LEU A 148 " ideal model delta sigma weight residual 110.88 117.65 -6.77 1.57e+00 4.06e-01 1.86e+01 angle pdb=" N TRP A 581 " pdb=" CA TRP A 581 " pdb=" C TRP A 581 " ideal model delta sigma weight residual 112.54 107.45 5.09 1.22e+00 6.72e-01 1.74e+01 angle pdb=" C THR A 313 " pdb=" CA THR A 313 " pdb=" CB THR A 313 " ideal model delta sigma weight residual 110.92 116.56 -5.64 1.59e+00 3.96e-01 1.26e+01 angle pdb=" N ALA A 307 " pdb=" CA ALA A 307 " pdb=" C ALA A 307 " ideal model delta sigma weight residual 111.36 107.56 3.80 1.09e+00 8.42e-01 1.22e+01 ... (remaining 7743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.39: 3197 18.39 - 36.78: 126 36.78 - 55.17: 19 55.17 - 73.56: 5 73.56 - 91.95: 2 Dihedral angle restraints: 3349 sinusoidal: 1293 harmonic: 2056 Sorted by residual: dihedral pdb=" C LEU A 653 " pdb=" N LEU A 653 " pdb=" CA LEU A 653 " pdb=" CB LEU A 653 " ideal model delta harmonic sigma weight residual -122.60 -135.73 13.13 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C TYR A 233 " pdb=" N TYR A 233 " pdb=" CA TYR A 233 " pdb=" CB TYR A 233 " ideal model delta harmonic sigma weight residual -122.60 -135.50 12.90 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" N TYR A 233 " pdb=" C TYR A 233 " pdb=" CA TYR A 233 " pdb=" CB TYR A 233 " ideal model delta harmonic sigma weight residual 122.80 134.68 -11.88 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 3346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 769 0.112 - 0.223: 72 0.223 - 0.335: 24 0.335 - 0.447: 8 0.447 - 0.559: 2 Chirality restraints: 875 Sorted by residual: chirality pdb=" CA TYR A 233 " pdb=" N TYR A 233 " pdb=" C TYR A 233 " pdb=" CB TYR A 233 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" CA LEU A 653 " pdb=" N LEU A 653 " pdb=" C LEU A 653 " pdb=" CB LEU A 653 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA THR A 313 " pdb=" N THR A 313 " pdb=" C THR A 313 " pdb=" CB THR A 313 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 872 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 137 " 0.045 2.00e-02 2.50e+03 4.11e-02 4.22e+01 pdb=" CG TRP A 137 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 TRP A 137 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP A 137 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 137 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 137 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 137 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 137 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 137 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 622 " 0.040 2.00e-02 2.50e+03 3.92e-02 3.08e+01 pdb=" CG TYR A 622 " -0.096 2.00e-02 2.50e+03 pdb=" CD1 TYR A 622 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 622 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 622 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 622 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 622 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 622 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 653 " -0.027 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C LEU A 653 " 0.094 2.00e-02 2.50e+03 pdb=" O LEU A 653 " -0.036 2.00e-02 2.50e+03 pdb=" N GLN A 654 " -0.031 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1664 2.82 - 3.34: 5640 3.34 - 3.86: 9214 3.86 - 4.38: 10812 4.38 - 4.90: 18515 Nonbonded interactions: 45845 Sorted by model distance: nonbonded pdb=" OH TYR A 630 " pdb=" OE1 GLU A 666 " model vdw 2.304 3.040 nonbonded pdb=" O GLY A 51 " pdb=" ND2 ASN A 445 " model vdw 2.307 3.120 nonbonded pdb=" OH TYR A 449 " pdb=" OE2 GLU A 454 " model vdw 2.328 3.040 nonbonded pdb=" O THR A 136 " pdb=" OG SER A 140 " model vdw 2.338 3.040 nonbonded pdb=" OD1 ASP A 420 " pdb=" NZ LYS A 424 " model vdw 2.343 3.120 ... (remaining 45840 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: 2.860 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: 0.020 Set scattering table: 0.020 Process input model: 5.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 : 0.007 0.072 5687 Z= 0.432 Angle : 0.930 8.022 7753 Z= 0.570 Chirality : 0.088 0.559 875 Planarity : 0.012 0.081 969 Dihedral : 10.875 91.952 2022 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.27 % Favored : 96.59 % Rotamer: Outliers : 0.35 % Allowed : 3.19 % Favored : 96.46 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.30), residues: 704 helix: -0.27 (0.23), residues: 441 sheet: -0.09 (0.91), residues: 31 loop : -1.01 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.076 0.004 ARG A 115 TYR 0.096 0.006 TYR A 622 PHE 0.045 0.002 PHE A 356 TRP 0.108 0.004 TRP A 137 HIS 0.027 0.003 HIS A 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.43 ( 5685) covalent geometry : angle 0.92101 / 0.57 ( 7748) SS BOND : bond 0.00428 / 0.23 ( 1) SS BOND : angle 2.98555 / 1.74 ( 2) hydrogen bonds : bond 0.12124 / 8.27 ( 337) hydrogen bonds : angle 6.14774 / 4.51 ( 993) link_NAG-ASN : bond 0.01264 / 0.67 ( 1) link_NAG-ASN : angle 6.14920 / 2.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.168 Fit side-chains REVERT: A 198 LEU cc_start: 0.8722 (mt) cc_final: 0.8477 (mt) REVERT: A 348 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8640 (tm) REVERT: A 350 MET cc_start: 0.8632 (tpt) cc_final: 0.8324 (tpt) REVERT: A 545 ASP cc_start: 0.7805 (m-30) cc_final: 0.7442 (m-30) outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 0.0400 time to fit residues: 3.6372 Evaluate side-chains 45 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** B 11 GLN ** 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 = 0.3345 r_free = 0.3345 target = 0.089235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069628 restraints weight = 11458.342| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.05 r_work: 0.2880 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5687 Z= 0.134 Angle : 0.536 7.557 7753 Z= 0.270 Chirality : 0.040 0.187 875 Planarity : 0.004 0.040 969 Dihedral : 6.464 82.236 820 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.02 % Rotamer: Outliers : 0.53 % Allowed : 5.84 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.09 (0.32), residues: 704 helix: 1.58 (0.24), residues: 442 sheet: -0.19 (0.94), residues: 31 loop : -0.79 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.008 0.001 TYR A 622 PHE 0.009 0.001 PHE A 262 TRP 0.019 0.001 TRP A 137 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5685) covalent geometry : angle 0.52773 / 0.27 ( 7748) SS BOND : bond 0.00422 / 0.22 ( 1) SS BOND : angle 1.76164 / 1.04 ( 2) hydrogen bonds : bond 0.04325 / 2.87 ( 337) hydrogen bonds : angle 4.36688 / 3.30 ( 993) link_NAG-ASN : bond 0.00466 / 0.25 ( 1) link_NAG-ASN : angle 4.66660 / 2.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.220 Fit side-chains REVERT: A 198 LEU cc_start: 0.8923 (mt) cc_final: 0.8720 (mt) REVERT: A 350 MET cc_start: 0.8688 (tpt) cc_final: 0.8394 (tpt) REVERT: A 545 ASP cc_start: 0.8406 (m-30) cc_final: 0.8186 (m-30) outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 0.0440 time to fit residues: 3.3812 Evaluate side-chains 42 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 68 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** 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 = 0.3341 r_free = 0.3341 target = 0.089040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069390 restraints weight = 11379.917| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.05 r_work: 0.2875 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5687 Z= 0.121 Angle : 0.502 6.609 7753 Z= 0.248 Chirality : 0.039 0.176 875 Planarity : 0.004 0.043 969 Dihedral : 5.985 73.246 818 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Rotamer: Outliers : 0.71 % Allowed : 6.90 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.33), residues: 704 helix: 2.01 (0.25), residues: 444 sheet: -0.39 (0.92), residues: 31 loop : -0.92 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 652 TYR 0.021 0.001 TYR A 643 PHE 0.007 0.001 PHE A 422 TRP 0.015 0.001 TRP A 569 HIS 0.004 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5685) covalent geometry : angle 0.49586 / 0.25 ( 7748) SS BOND : bond 0.00459 / 0.24 ( 1) SS BOND : angle 1.53593 / 0.90 ( 2) hydrogen bonds : bond 0.03735 / 2.49 ( 337) hydrogen bonds : angle 4.03036 / 3.05 ( 993) link_NAG-ASN : bond 0.00370 / 0.19 ( 1) link_NAG-ASN : angle 3.72768 / 1.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.202 Fit side-chains REVERT: A 350 MET cc_start: 0.8652 (tpt) cc_final: 0.8362 (tpt) outliers start: 4 outliers final: 1 residues processed: 40 average time/residue: 0.0414 time to fit residues: 2.7544 Evaluate side-chains 39 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 40.0000 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** B 11 GLN ** 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 = 0.3328 r_free = 0.3328 target = 0.087927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.068116 restraints weight = 11567.910| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.06 r_work: 0.2857 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5687 Z= 0.165 Angle : 0.513 6.019 7753 Z= 0.254 Chirality : 0.040 0.189 875 Planarity : 0.004 0.043 969 Dihedral : 5.786 67.874 818 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.45 % Rotamer: Outliers : 1.06 % Allowed : 7.26 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.33), residues: 704 helix: 2.03 (0.25), residues: 447 sheet: -0.48 (0.90), residues: 31 loop : -1.00 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 490 TYR 0.009 0.001 TYR A 567 PHE 0.008 0.001 PHE A 262 TRP 0.017 0.001 TRP A 569 HIS 0.003 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 5685) covalent geometry : angle 0.50775 / 0.25 ( 7748) SS BOND : bond 0.00513 / 0.27 ( 1) SS BOND : angle 1.85030 / 1.08 ( 2) hydrogen bonds : bond 0.03774 / 2.50 ( 337) hydrogen bonds : angle 3.96829 / 3.01 ( 993) link_NAG-ASN : bond 0.00378 / 0.20 ( 1) link_NAG-ASN : angle 3.34336 / 1.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.248 Fit side-chains REVERT: A 502 MET cc_start: 0.7777 (ppp) cc_final: 0.6762 (ppp) outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 0.0706 time to fit residues: 4.4442 Evaluate side-chains 41 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 519 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.089153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069273 restraints weight = 11633.238| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.09 r_work: 0.2879 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5687 Z= 0.116 Angle : 0.484 9.634 7753 Z= 0.236 Chirality : 0.039 0.170 875 Planarity : 0.004 0.053 969 Dihedral : 5.530 59.722 818 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.27 % Favored : 96.59 % Rotamer: Outliers : 0.53 % Allowed : 8.85 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.50 (0.32), residues: 704 helix: 2.12 (0.25), residues: 444 sheet: -0.53 (0.90), residues: 31 loop : -1.08 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.008 0.001 TYR A 674 PHE 0.007 0.001 PHE A 422 TRP 0.016 0.001 TRP A 569 HIS 0.002 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5685) covalent geometry : angle 0.48006 / 0.23 ( 7748) SS BOND : bond 0.00478 / 0.25 ( 1) SS BOND : angle 1.48079 / 0.87 ( 2) hydrogen bonds : bond 0.03402 / 2.26 ( 337) hydrogen bonds : angle 3.84764 / 2.93 ( 993) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 3.04588 / 1.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.202 Fit side-chains REVERT: A 350 MET cc_start: 0.8646 (tpp) cc_final: 0.8345 (tpt) REVERT: A 502 MET cc_start: 0.7672 (ppp) cc_final: 0.7004 (ppp) outliers start: 3 outliers final: 0 residues processed: 40 average time/residue: 0.0472 time to fit residues: 3.1235 Evaluate side-chains 38 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.0030 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** 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 = 0.3358 r_free = 0.3358 target = 0.089889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.070083 restraints weight = 11380.559| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.04 r_work: 0.2895 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5687 Z= 0.095 Angle : 0.469 6.335 7753 Z= 0.229 Chirality : 0.038 0.159 875 Planarity : 0.004 0.049 969 Dihedral : 5.322 53.916 818 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.27 % Favored : 96.59 % Rotamer: Outliers : 0.35 % Allowed : 9.73 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.59 (0.32), residues: 704 helix: 2.22 (0.25), residues: 445 sheet: -0.56 (0.89), residues: 31 loop : -1.13 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.008 0.001 TYR A 674 PHE 0.007 0.001 PHE A 422 TRP 0.014 0.001 TRP A 569 HIS 0.002 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 5685) covalent geometry : angle 0.46541 / 0.23 ( 7748) SS BOND : bond 0.00494 / 0.26 ( 1) SS BOND : angle 1.48126 / 0.87 ( 2) hydrogen bonds : bond 0.03189 / 2.12 ( 337) hydrogen bonds : angle 3.77148 / 2.86 ( 993) link_NAG-ASN : bond 0.00101 / 0.05 ( 1) link_NAG-ASN : angle 2.88531 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.208 Fit side-chains REVERT: A 350 MET cc_start: 0.8612 (tpp) cc_final: 0.8298 (tpt) REVERT: A 502 MET cc_start: 0.7759 (ppp) cc_final: 0.7106 (ppp) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.0515 time to fit residues: 3.2521 Evaluate side-chains 38 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** 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 = 0.3356 r_free = 0.3356 target = 0.089799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.069996 restraints weight = 11480.775| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.07 r_work: 0.2898 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5687 Z= 0.100 Angle : 0.462 5.826 7753 Z= 0.226 Chirality : 0.038 0.157 875 Planarity : 0.004 0.050 969 Dihedral : 5.194 49.552 818 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Rotamer: Outliers : 0.71 % Allowed : 8.85 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 704 helix: 2.29 (0.25), residues: 445 sheet: -0.66 (0.89), residues: 31 loop : -1.17 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 448 TYR 0.008 0.001 TYR A 674 PHE 0.007 0.001 PHE A 422 TRP 0.014 0.001 TRP A 569 HIS 0.002 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 5685) covalent geometry : angle 0.45875 / 0.22 ( 7748) SS BOND : bond 0.00478 / 0.25 ( 1) SS BOND : angle 1.36166 / 0.79 ( 2) hydrogen bonds : bond 0.03132 / 2.08 ( 337) hydrogen bonds : angle 3.72525 / 2.83 ( 993) link_NAG-ASN : bond 0.00078 / 0.04 ( 1) link_NAG-ASN : angle 2.72632 / 1.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.145 Fit side-chains REVERT: A 350 MET cc_start: 0.8612 (tpp) cc_final: 0.8286 (tpt) REVERT: A 456 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8825 (tt) REVERT: A 502 MET cc_start: 0.7784 (ppp) cc_final: 0.7211 (ppp) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.0457 time to fit residues: 3.0526 Evaluate side-chains 40 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 519 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** 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 = 0.3363 r_free = 0.3363 target = 0.090285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.070553 restraints weight = 11294.341| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.05 r_work: 0.2906 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5687 Z= 0.095 Angle : 0.465 8.704 7753 Z= 0.226 Chirality : 0.038 0.151 875 Planarity : 0.004 0.052 969 Dihedral : 5.107 46.785 818 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.27 % Favored : 96.59 % Rotamer: Outliers : 0.53 % Allowed : 9.73 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.33), residues: 704 helix: 2.36 (0.25), residues: 445 sheet: -0.74 (0.89), residues: 31 loop : -1.19 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 448 TYR 0.008 0.001 TYR A 674 PHE 0.007 0.001 PHE A 422 TRP 0.013 0.001 TRP A 569 HIS 0.002 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 5685) covalent geometry : angle 0.46179 / 0.23 ( 7748) SS BOND : bond 0.00492 / 0.26 ( 1) SS BOND : angle 1.44168 / 0.84 ( 2) hydrogen bonds : bond 0.03030 / 2.02 ( 337) hydrogen bonds : angle 3.69212 / 2.81 ( 993) link_NAG-ASN : bond 0.00020 / 0.01 ( 1) link_NAG-ASN : angle 2.59583 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.258 Fit side-chains REVERT: A 350 MET cc_start: 0.8599 (tpp) cc_final: 0.8279 (tpt) REVERT: A 456 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8822 (tt) REVERT: A 502 MET cc_start: 0.7759 (ppp) cc_final: 0.7206 (ppp) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.0435 time to fit residues: 3.0578 Evaluate side-chains 41 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 456 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 0.0000 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 54 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 overall best weight: 0.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** 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 = 0.3366 r_free = 0.3366 target = 0.090328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070503 restraints weight = 11348.151| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.03 r_work: 0.2906 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5687 Z= 0.097 Angle : 0.474 7.387 7753 Z= 0.231 Chirality : 0.038 0.151 875 Planarity : 0.004 0.055 969 Dihedral : 5.083 45.678 818 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.69 % Favored : 96.16 % Rotamer: Outliers : 0.71 % Allowed : 10.80 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.72 (0.33), residues: 704 helix: 2.39 (0.25), residues: 445 sheet: -0.72 (0.89), residues: 31 loop : -1.20 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 448 TYR 0.008 0.001 TYR A 674 PHE 0.007 0.001 PHE A 422 TRP 0.013 0.001 TRP A 569 HIS 0.002 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 5685) covalent geometry : angle 0.47110 / 0.23 ( 7748) SS BOND : bond 0.00500 / 0.26 ( 1) SS BOND : angle 1.44187 / 0.84 ( 2) hydrogen bonds : bond 0.03031 / 2.03 ( 337) hydrogen bonds : angle 3.69109 / 2.80 ( 993) link_NAG-ASN : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : angle 2.48659 / 1.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.132 Fit side-chains REVERT: A 350 MET cc_start: 0.8587 (tpp) cc_final: 0.8265 (tpt) REVERT: A 456 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8819 (tt) REVERT: A 502 MET cc_start: 0.7761 (ppp) cc_final: 0.7243 (ppp) outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 0.0360 time to fit residues: 2.4739 Evaluate side-chains 38 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 456 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 0.0270 chunk 41 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** 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 = 0.3365 r_free = 0.3365 target = 0.090245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.070469 restraints weight = 11485.679| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.05 r_work: 0.2902 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5687 Z= 0.104 Angle : 0.473 7.533 7753 Z= 0.231 Chirality : 0.039 0.184 875 Planarity : 0.004 0.055 969 Dihedral : 5.073 45.150 818 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Rotamer: Outliers : 0.35 % Allowed : 10.97 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.74 (0.33), residues: 704 helix: 2.40 (0.25), residues: 445 sheet: -0.67 (0.88), residues: 31 loop : -1.19 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 293 TYR 0.008 0.001 TYR A 674 PHE 0.006 0.001 PHE A 422 TRP 0.012 0.001 TRP A 569 HIS 0.002 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 ( 5685) covalent geometry : angle 0.47062 / 0.23 ( 7748) SS BOND : bond 0.00559 / 0.29 ( 1) SS BOND : angle 1.53299 / 0.90 ( 2) hydrogen bonds : bond 0.03084 / 2.07 ( 337) hydrogen bonds : angle 3.70127 / 2.81 ( 993) link_NAG-ASN : bond 0.00022 / 0.01 ( 1) link_NAG-ASN : angle 2.38528 / 1.13 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.170 Fit side-chains REVERT: A 350 MET cc_start: 0.8586 (tpp) cc_final: 0.8268 (tpt) REVERT: A 456 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8819 (tt) REVERT: A 502 MET cc_start: 0.7772 (ppp) cc_final: 0.7255 (ppp) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.0431 time to fit residues: 2.6875 Evaluate side-chains 37 residues out of total 604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 456 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 24 optimal weight: 0.0170 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 HIS ** 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 = 0.3359 r_free = 0.3359 target = 0.090334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.070497 restraints weight = 11396.004| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.09 r_work: 0.2897 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5687 Z= 0.100 Angle : 0.474 7.587 7753 Z= 0.232 Chirality : 0.039 0.189 875 Planarity : 0.004 0.054 969 Dihedral : 5.058 44.020 818 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 0.35 % Allowed : 11.33 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.80 (0.33), residues: 704 helix: 2.44 (0.25), residues: 445 sheet: -0.62 (0.89), residues: 31 loop : -1.17 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 448 TYR 0.008 0.001 TYR A 674 PHE 0.006 0.001 PHE A 422 TRP 0.012 0.001 TRP A 569 HIS 0.002 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 5685) covalent geometry : angle 0.47142 / 0.23 ( 7748) SS BOND : bond 0.00534 / 0.28 ( 1) SS BOND : angle 1.48750 / 0.87 ( 2) hydrogen bonds : bond 0.03045 / 2.04 ( 337) hydrogen bonds : angle 3.68388 / 2.80 ( 993) link_NAG-ASN : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : angle 2.32861 / 1.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1230.78 seconds wall clock time: 21 minutes 46.35 seconds (1306.35 seconds total)